[ add | alias | align | Append command | assign | break | build | call | center | clear | color | Color chemical | Color accessibility | Compare | compress | connect | continue | convert | copy | crypt | Date array | Delete | display | edit | elseif | endfor | endif | endmacro | Enumerate charge | Enumerate chiral | Enumerate tautomer | Enumerate library | endwhile | exit | find | fix | for | fork | fprintf | function | Global | goto | group | Gui | help | history | if | info | keep | join tables | Learn | Mlr | Learn ann | Link grob | Link group | Link variables | Link ms2ali | list | List binary | List database | list directory | list molcart | load | Macro | make | minimize | menu | modify | Modify rotate | Modify chem | montecarlo | move | pause | plot | Plot area | predict | print | Print bar | printf | print image | Query molcart | quit | randomize | read | rename | return | rotate | select | Set | show | sort | split | sprintf | store | ssearch | strip | superimpose | Superimpose minimize | Sys | test | then | transform | translate | undisplay | undisplay window | unfix | wait | web | while | write ]

ICM commands have a certain structure:

• they use command words from this list: align assign build clear compare connect convert copy compress crypt delete display edit enumerate exit exclude filter find fix fork fprintf group gui keep learn load make menu minimize modify montecarlo move pause plot predict print printf quit query randomize read redo refresh rename restore rotate select set show sort split sprintf ssearch store strip superimpose test transform translate undisplay undo unfix unselect unix wait write
  alias antialias center color help history link list macro model sql web
  accessibility alignment amber angle area aselection atom axis background ball base bar bfactor bond born boundary box catalog cavity cell chain charge cmyk column command comment comp_matrix conf cpk csd cursor chemical cistrans database distance directory disulfide dot drestraint energy error evolution factor field filename font foreground frame function gamess genome gradient grid grob hbond header html hydrogen iarray icmdb idb image index info input integer intensity inverse iupac json kernel key label library logical loop limit margin material map matrix memory merit mol mol2 moldb molcart molecule movie molsar name nucleotide object occupancy oracle origin output page parray pattern peptide pipe pdb plane postscript potential preference preview problem profile project property prosite protein pharmacophore rarray reaction real regression reflection residue resolution ring rgb ribbon regexp rainbow sarray segment selection selftether separator sequence session site size skin slide salt solution stack stdin stdout stick sstructure string surface symmetry system svariable table term tether texture topology torsion trajectory transparent tree type unknown user variable vector version view virtual volume vrestraint vselection water weight window wire xstick
  add all append auto auxiliary binary bold bw cartesian clash chiral dash exact join fast fasta flat formal format full gcg gif global graphic heavy identity italic jpeg last left local mmcif mmff msf mute new none nosort number off on only pca pir pmf png pseudo pov reverse right similarity simple sln smiles smooth solid static stereo swiss targa tautomer underline unique wavefront xplor
• the they arguments consisting of constants, named shell variables or expressions including functions, e.g. display ribbon Res(Sphere( a_H a_A 7.6 ))
• the order of arguments of different data type is arbitrary
• at the end of the command one may have a list of additional shell variables that will be redefined temporarily only for the duration of this command, e.g. montecarlo v_//x* mncalls=200 mncallsMC=20000 temperature=1000.
• several commands in one line can be separated by a semicolon
• commands can return certain shell variables, like i_out , i_2out, r_out , l_out , s_out , R_out , as_out .. with useful output
• to suppress command output redefine those shell variables: l_info=no or l_warn=no (for some commands there is also a mute option )

add

[ Add column | Add matrix | Add slide | Add table ]

A family of commands adding things. Some commands use append syntax instead It is also used as an option equivalent to append in write command.

add one or several columns or header elements to an existing table

[ Add column function ]

Adding a single column/header you may add a column (or columns) to an existing table T or create a new one if the specified name does not exist.

add column T I|R|S|P|i|r|s [name= s [append|delete] ] [index= i_pos] [mute] [local]

add header T I|R|S|P|i|r|s|M|etc [name= s [append|delete] ] [mute] [local]

(to add a row see add table args )

Adding multiple column/headers

add column T I|R|S|P|i|r|s I|R|S|P|i|r|s .. [name= S [append|delete]] [index= i_pos ] [mute] [local]

add header T I|R|S|P|i|r|s|M|etc I|R|S|P|i|r|s|M|etc .. [name= S .. ] [index= i_pos ] [mute] [local]

this command adds one or several columns to an existing table in the i_pos column (in other words if you want you column to be in the 2nd position, specify 2 as an argument). The columns are append to the end of the table by default. If the table does not exist the command will create a new table.

It an integer, string, or real are specified as an argument instead of a column-array, this value is multipled to create a column of the appropriate size.

Options:

• append: if the name option is specified prevents overwriting the column with the same name, instead modifies the provided name (e.g. 'A' -> 'A_1' )
• delete: if the name option is specified overwrites the column with the same name. Without delete (default) it will be overwritten only if the data type is the same.
• mute : The mute option suppresses the info (equivalent to temporarily setting l_info=no ).
• local : for use in macros ans shell functions: allows for local tables independent from tables with the same name at higher levels.

Examples:

add column t {1 2 3} # create a new table
add header t "A new table" name="title" # add a string to the header section
add column t {"a","b","c"} name="AA" # column AA is appended
add column t {"x","y","z"} index = 2 
# adding a chemical array
add column t Parray({"CC","CC(O)=O","CCO"} smiles) name = "mol" index = 1

# adding multiple arrays
add column t {1 2 3} {3 2 1} {"a","b","c"} Parray({"CC","CC(O)=O","CCO"} smiles) name={"A","B","C","mol"}
t
 #>T t
 #>-A-----------B-----------C-----------mol--------
    1           3           a          "CC"
    2           2           b          "CC(O)=O"
    3           1           c          "CCO"

The columns can also be functions, e.g.

add column t {1. 2. 3.} {2 3 4}
add column t function="A+B" name="AplusB"
add column t function="Log(A,10)" name="log10A"

Use add column inside a macro:

macro ResAreas  rs_sel 
  rs_sel = Res( rs_sel & a_*.!W )
  show surface area Mol(rs_sel) Mol(rs_sel)
  add column t Name(Res(rs_sel) full) Area(Res(rs_sel)) Area( a_1.A/A )/Area( a_1.A/A type) local name={"sel","area","rel_area"}
  set format t.sel "<!--icmscript name=\"1\"\ndisplay xstick %1\ncolor xstick cpk %1 & a_*.//c* green\ndisplay residue label %1\n\n\n--><a href=#_>%1</a>"
  if(Type(resAreas)!="unknown") delete resAreas
  rename t "resAreas"
  keep resAreas
endmacro

See also: move column , add column function

Add columns using internal functions in dynamic or static manner

add column T function=s_expression [static] [name=s] [index= i_pos]

By default the column is added in a dynamic manner so that it can be recalculated from other columns. Option static adds the new column as a value and will not allow for the recalculation. Adds a column a string that contains an expression or a reference to one of three sources of functions:

• one of a few fast-access internal functions listed below, e.g. function="Sqrt"
• one of a thousand built-in ICM-shell functions (described in this manual), e.g. function="Icm::Min(COL)"
• an arbitrary user-defined ICM-shell function loaded from a file or ~.icm/user_startup.icm file. E.g. function="myfunc(A)"

which may contain operations with other columns in the same table. The generating expression information is attached to the column, which allows one to recalculate the values in the column using the same expression. The following functions are supported:

Basic arithmetical operations on columns are supported, examples:

add column t {1. 2. 3.} {1. 2. 3.}
add column t function="A+B" name="C"
add column t function="A-B" name="D"
add column t function="A*B" name="E"
add column t function="A/B" name="F"
add column t function="A**0.5 + B**0.5" name="G"
build column t
show t

 Ceil, Floor, Log,  Sqrt, Sign, String, Power

add column t {1. 2. 3.} {1. 2. 3.}
add column t function="Sqrt(A)" name="C"

Chemical functionsThe following internal functions (not ICM-shell functions) are allowed in function=".." expressions (eg add column t function="MolPSA(mol)":

Examples of chemical functions usage:

add column t Chemical("CCO"//"CCCCO"//"CCCC#N")
add column t function="Nof_Atoms(mol,'*')" name="nof1"  # all atoms
add column t function="Nof_Atoms(mol,'[!H]')" name="nof2" 
add column t function="Nof_Atoms(mol,'[C,O]')" name="nof3" 
add column t function="Nof_Atoms(mol,'[H]')" name="nof4" 
add column t function="MolWeight(mol)" name="molWeight"
add column t function="MolLogP(mol)"   name="molLogP"
add column t function="MolLogS(mol)"   name="molLogS"
add column t function="MolPSA(mol)"    name="molPSA"
add column t function="MolVolume(mol)" name="molVolume"
add column t function="MoldHf(mol)"    name="moldHf"
add column t function="calcBBBScore(mol)" index=2 name="bbbScore" append vector   
add column t function="MolSynth(mol)" index=2 name="molSynth" append vector   

User-defined functions

A user can defined custom function to be used in column formula expression directly : function="userFunctionName(columnArgument)"

Example:

function ligStrain( P_chem )  # returns strain for a given 3D chemical
  vwMethod = "exact"
  dielConst = 2.
  read mol P_chem name="LIGSTRAIN"
  build hydrogen
  set type charge mmff
  convert auto 
  minimize cartesian "mmff" mncalls=1
  newE = Energy("ener")
  minimize cartesian "mmff" 5000
  baseE = Energy("ener")
  r_ligandStrain = newE - baseE
  delete a_
  return r_ligandStrain
endfunction

# assumes that t_3D exists and contains 3D chemicals in the mol column
add column t_3D function="ligStrain(mol)" name="strain"   # strain for every row in the table

ICM built-in shell functions.

ICM build-in functions can also be used in the expression with "Icm::" prefix.

Example:

add column drugs function = "Icm::Sum(Icm::Unique(Icm::Sort(Icm::Sarray(A.dosages.dosage:route))),',')" name="route"

Recalculating.To recalculate use the build column column_name command.

Examples:

add column T Chemical( {"c1(c(nc(N)nc1O)O)N", "c1c[nH]c2C(N=C(N)Nc12)=O"} ) name="mol"
add column T function="MolWeight(mol)" name="MW"
add T # add new row
T.mol[3] = Chemical("CC")
#
build column T.MW # recalculate mol. weights, setting the value for the new row

add column T2 {1 2 3} {4 5 6}
add column T2 function= "A+B"  # sum of two columns

See also: build column to update values, Parray ( X [ s_func ] ) to add a fixed column

Adding real arrays as matrix rows

add matrix [ M ] R|M2

adds a matching row R or a matrix with the matching number of columns to matrix M, by stacking extra rows at the bottom. If the matrix does not exist it is created with the default name (the name is returned in s_out ) Example:

add matrix M {1. 2.} # creates new matrix M
add matrix M {3. 3.} # adds a row
show M
 #>M M
 1. 2. 
 3. 3.
add matrix M Matrix(2) # adds two rows

add slide to a slideshow.

add slide [i_posInCurrentSlideshow] [s_slideTitle] [comment = s_slideComment] [ display= "-option|-option2" ]

adds a slide to the slideshow table. This table contains one parray, called slideshow.slides . If the slide position is not specified the slide will be added to the end. Alternatively, it will be inserted after the specified i_posInCurrentSlideshow

Normally the slide is saved with window layout, and graphical parameters. Those can be ignored if you add the display="-option" flag (all listed properties are 'on' by default).

• "-layout" # ignores the window/panel layout
• "-smooth" # ignores smooth view transitions between slides
• "-add" # do not overwrite the previous slide views, just add to it
• "-gf" # ignore graphical representations, inherit them
• "-color" # ignore colors , inherit them
• "-labeloffs" # do not display labels
• "-viewpoint" # ignore viewpoint changes
• "-graphopt" #
• "-mol" # do not display the chem-table window
• "-grob" # do not display grobs
• "-map" # do not display maps
• "-all" # switches off all the above properties

Example:

build string "ala ala ala"
display ribbon a_ 
display xstick a_/12,13 magenta
add slide "My View" comment = "Two magenta residues" display="-layout" 
undisplay # hide all
# wait..
display slide "My View" # bring it back

See also: display slide , Slide

Add / insert table rows. Append tables.

add T_1 [ i_RowNumber ] [ T_2 | row_selection | number=i_nofRows ] [ simple ]
add/insert rows (or another table with the same coloumns) to table T_1 at the target row position i_RowNumber . Use 1 (one) if you need to insert the first line. If the second table or selection is not provided, the command adds an empty row. In this case you can add number option to specify the number of rows to add/insert. The row_selection can contain rows from the same table or from a different table with a matching column structure. In the latter case, the columns may be matched by their names regardless of column order. Default values are inserted for all absent columns. The defaults for an empty line are empty string or zero value for strings or numbers, respectively. The target position will then correspond to the index of the first inserted row.

simple option toggle column matching order 'by position' instead of default 'by name'.

From version 3.6-1e the add tableName command also returns the current row as i_out .

Examples:

 
group table t {1 2 3} "a" {"b","d","e"} "b" 
show t 
 #>T t 
 #>-a-----------b---------- 
    1           b 
    2           d 
    3           e 
 
add t 1 # insert empty line before 1st  
show t 
 #>T t 
 #>-a-----------b---------- 
    0           ""  
    1           b 
    2           d 
    3           e 
 
group table t {1 2 3} "a" {"b","d","e"} "b" # recreate the table 
add t 3 t[1]  # insert a duplicate of 1st row after the 2nd  
show t
 #>T t 
 #>-a-----------b---------- 
    1           b 
    2           d 
    1           b 
    3           e 
 
group table t {1 2 3}  "a"  {"b","d","e"} "b"  # recreate the table 
group table tt {1 2 3} "c" {"b","d","e"} "b" {4 5 6} "a" # another table 
# order is diffferent, extra column present  
add t 3 tt[1:2]  # or add t 3 tt.aa<3  
show t 
 #>T t 
 #>-a-----------b---------- 
    1           b 
    2           d 
    4           b 
    5           d 
    3           e 

 
 alias seq sequence                    # seq will invoke sequence  
 alias delete seq                      # delete alias name seq  
 alias dsb display a_//ca,c,n          # abbreviate several words to  
                                       # reduce typing efforts  
                                       # aliases with arguments  
 alias NORM ($1-Mean($1))/Rmsd($1) 
 show NORM {6,7,8,4,6,5,6,7,5,6}       # make sure there is no space 

[ Align number chemical | Align res numbers | Align sequence | Align fragments | Align 3D | Align 3D heavy ]

align number chemical ms_het_molecules

Examples:

read pdb "3gvu"
align number chemical a_H.  # rename atoms in both ligands 

align number: renumber residues sequentially

align number rs_residuesToBeRenumbered i_first|s|I|S [molecule]
align number ms_chainsToBeRenumbered [ i_firstNumber ]
renumber selected residues, or residues in selected molecules or objects sequentially in all of them from starting one or the specified first number. May be useful to deal with messy numbering in some pdb-files. Option molecule will start numbers from 1 or i_first in each molecule. Chain ids are also allowed, e.g. set number a_/13 "13A". Multiple residues can be set with integer or string arrays of labels. If integer array contains the same numbers, e.g. 10,10,10 the labels will get the insertion characters, e.g. 10,10A,10B .

Examples:

 
 read pdb "1crn" 
 align number a_1            # renumber all res. 1 to N 
 align number a_1/10:20 101  # just the selected residues from 101 
 align number a_1       101  # renumber all res. 101 to 100+N 
 read pdb "2ins"
 align number a_/* 1
 align number a_/* 1 molecule # each chain starts from 1

 
 seqmaster = Sequence("ACDEFGHIKLMNPQRST") 
 build string   "DEFGH-----PQRST"  # dashes are skipped    
 make sequence a_1 name="seqmodel"   # sequence is auto-linked 
 a = Align(seqmodel,seqmaster)       # linked alignment 
 align number a_1 seqmaster 
 # Info> residues of a_def.m renumbered by sequence 'seqmaster' from alignment 'a'    
 display residue label  

align sequence [selection] | seq1 seq2 .. | seedSequence [ min_seqID (20.)] [ name=s ]
make a multiple alignment of specified sequences. The sequence group may result from the group sequence s_groupName command. The input arguments include the following:

• seq1 seq2 ... : explicitly specified
• sequence : all sequences in the shell
• sequence selection : all sequences selected in GUI
• seqGroup : sequences grouped together previously
• seedSequence : sequences in the shell similar to the specified with optional min_seqID (default 20%).

For pairwise alignment use the Align( seq1 seq2 ) function. The algorithm includes the following steps (inspired by corridor discussions with Des Higgins, Toby Gibson and Julie Thompson ):

1. align all sequence pairs with the ICM ZEGA algorithm, and calculate pairwise distances between each pair of aligned sequence with the Dayhoff formula, e.g. the distance between two identical sequences will be 0. , while the distance between two 30% different sequences will be around 0.5. The distance goes to an arbitrary number of 10. for completely unrelated sequences. The distance matrix D_ij can later be extracted from the alignment with the Distance( ali_ ) function.
2. build an evolutionary tree from D_ij with the "neighbor-joining algorithm" of Saitou, N., Nei, M. (1987) to determine the order of the alignment and calculate relative weights of sequences and profiles from the branch lengths. The tree will be saved in the file defined by the tree= s or filename= s option . Starting from version 3.5-2 the aligTree.eps file is NO LONGER saved by default). The so-called Newick tree description string will be saved in s_out .
3. traverse the tree from top to bottom, aligning the closest sequences, sequence and profile or two profiles. After each Needleman and Wunsch alignment, build the profile.
4. generate the final neighbor-joining evolutionary tree and write the PostScript file with the tree to disk.

 
   read sequences s_icmhome+"zincFing"  
   list sequences               # see them, then ...  
   group sequence alZnFing      # group them, then ...  
   align alZnFing               # align them
   align alZnFing filename="znTree.eps"  # eps file with a tree

 
  read sequence swiss web "12S1_ARATH"
  read sequence swiss web "12S2_ARATH"
  group sequence arath
  align arath

[ sim4 ]

The procedure has the following steps: sequences are sorted by length the longest sequence is chosen as the seed sequence unless it is explicitly provided the longest sequence from the remaining set is aligned to the seed sequence using the external sim4 program. the output of this program is parsed and translated into the icm alignment the consensus sequence is created and becomes the master sequence the procedure is repeated until all the sequences are processed the multiple sequence alignment is further cleaned to compress spurious gaps when possible. This cleaning makes the consensus much more compact. The result of this command is best displayed with the show color ali_ command.

 
 read sequence "http://www.ncbi.nlm.nih.gov/UniGene/" + \ 
     "download.cgi?ID=5198&ORG=HsLINE=1" # 
 read sequence "../Hs5198" 
 group sequence unique u # squeeze out obvious redundancies and form group 'u' 
 align new u             # form multiple alignment and build consensus 
 show color u 

• filtering, group sequence unique=".."
• Trans ()
• show [color] ali_

This command finds the residue alignment (or residue-to-residue correspondence) for two arbitrary molecules having superposable parts of the backbone conformations. The structural alignment identification and optimal superposition is primarily based on the C-alpha-atom coordinates, but the sequence information can be added with a certain weight (the default value of r_seqWeight is 0.5 which was found optimal on a benchmark). The structural alignment algorithm is based on the ZEGA (zero-end-gap-alignment) dynamic programming procedure in which substitution scores for each i,j-pair of residues contain two terms:

• structural similarity in a i_windowSize window between two fragments surrounding residues i and j, respectively. This similarity is calculated as local Rmsd of the residue label atoms (these atoms are C-alpha atoms by default but can be reset to other atoms with the set label command, e.g. set label a_*.//cb ). If the option distance is specified the deviation of the interatomic distances between equivalent pairs of atoms (so called distance rmsd ) is calculated instead of a more traditional root-mean square deviation between atom coordinates of equivalent atoms. The latter method is less accurate but an order of magnitude faster.
• sequence similarity (if r_seqWeight > 0.). Average local sequence alignment score in the i_windowSize window is calculated for i,j-centered pair of fragments. In this sense this sequence similarity is different from the one used in pure sequence alignment (see the Align function), in which just the i,j residue pair is evaluated. The default value of r_seqWeight of 0.5 is rather mild (about a half of the structural signal).

• ali_out contains structural alignment (if sequences linked to the molecules do not exist, they will be created on the fly). The alignment can be further edited with the interactive alignment alignment editor.
• as_out contains the residue selection of the aligned residues in the first molecule
• as2_out contains the residue selection of the aligned residues in the second molecule
• M_out , the matrix of local structural/sequence similarity in a window is retained and can be visualized by:
• r_2out the result RMSD

Example:

 
read pdb "1ql6"
read pdb "2phk"
align a_1ql6. a_2phk.
make grob color 10.*M_out name="g_mat # x,y,z scales 
display g_mat 
# or 
plot area M_out display grid link 

• Align( seq_1 seq_2 distance|superimpose ). This function creates the first unrefined structural alignment as described above.
• find alignment which refines initial structural alignment.

 
  a = Align(... superimpose )  # superposition/RMSD based local str. alignment 
  a = Align(... distance    )  # distance RMSD based local str. alignment 
 
  find a superimpose 4.0 0.5 

 
  read pdb "1brl" 
  read pdb "1nfp" 
  rm a_*.!A 
  display a_*.//ca,c,n 
  color molecule a_*. 
  align a_2.1 a_1.1 
  center 
  show String(as_out) String(as2_out) 
  color red as_out 
  color blue as2_out 
  show ali_out 

• r_rmsd = 1. A
• i_windowSize = 15 residues
• i_minFragment = i_windowSize
• r_elongationWeight=0.1

 
 read pdb "4fxc" 
 read pdb "1ubq" 
 display a_*.//ca,c,n 
 color molecule a_*. 
 align heavy a_1.1 a_2.1 12 1.5 .1 
 center 
 load solution 2            # load the second best solution 
 color red  as_out 
 color blue as2_out 
 for i=1,10 
   load solution i 
   color molecule a_*. 
   color red  as_out 
   color blue as2_out 
   pause                     # rotate and hit 'return' 
 
 endfor 

[ Append sequence | Append stack | Append column ]

Appending sequences to a sequence group or an alignment

append ali_seqGroup seq_1 seq_2 .. .
appends sequences to a sequence group. This may be required if you formed a sequence group for future alignment or filtering/compression and you want to append additional sequences to it.

Examples:

 
read sequence group "bunch.seq" name="xx" # group xx is formed 
append xx my_seq  # appending your sequence to xx 
group xx unique   # filter out identical ones 
align xx 

read sequence swiss web "12S1_ARATH" 
read sequence swiss web "12S2_ARATH"
group sequence name="arath"
read sequence swiss web "14310_ARATH"
append arath 14310_ARATH
align arath

Appending a molecule or a ligand stack to an existing stack

append stack s_ligandStackFileName [i_maxConf]

append stack os_ligandObject

this command takes a stack which corresponds to a receptor object and appends each conformation in the stack with a conformation of the ligand. If the ligand conformation can be taken from either from a stack file, this command will combine each conf from the main stack with all conformations from the file. The i_maxConf argument will set the limit on how many conformations are taken from the ligand stack (i.e. append stack "lig.cnf" 1 will combine only the first conformation of the ligand )

If the second argument is an ICM object, each conf of the current stack will be extended with the variables from the ligand. Now the ligand object can be appended to the receptor object with the move command and the new combined object can use the expanded stack.

build string "ACDEF"  # the "ligand" peptide
rename a_ "Lig"
translate a_ {10. 0. 0.} # shift not to overlap with a_Rec.
montecarlo v_//!?vt*     # created Lig.cnf stack

build string "RSTVW"  # the "receptor" peptide
rename a_ "Rec"
montecarlo v_//!?vt*     # created Rec.cnf stack

move a_1. a_2.    # ligand must be the 1st argument
append stack "Lig.cnf" 4 # combine up to 4 best ligand confs
minimize stack    # minimizes each stack conf
load conf 1       # check them out

append two tables via two columns with matching values

append t1.A t2.B
Append rows of table t2 to table t1 by rows corresponding to unique column t2.B . The t1.A column values do not need to be unique.

 
group table people {"J","C","M"} "p" {"MS","MS","MS"} "orgid" 
group table orgs  {"MS"} "id" {"Molsoft"} "name" 
append people.orgid orgs.id 
people 
 #>T people 
 #>-p-----------orgid-------name------- 
    J           MS          Molsoft 
    C           MS          Molsoft 
    M           MS          Molsoft 

This command is a particular case of a more general join command.

See also the add table command for adding rows from a column with identical column structure (e.g. add t tt ).

assign

[ Assign sstructure | assign sstructure segment ]

assign sstructure rs [{ s_SecondaryStructTypeCharacter | s_SSstring }]
Manual assignment of a desired secondary structure annotation to a residue fragment

assign sstructure rs { s_SecondaryStructTypeCharacter | s_SSstring }
assign specified secondary structure to the selected residues rs_ , e.g.

 
 read pdb "1crn" 
 assign sstructure a_/* "_"  # make everything look like a coil 
 cool a_ 
 assign sstructure a_/1:10 "HHHH_EEEEE"   
 cool a_ 

This command does not change the geometry of the model, it only formally assigns secondary structure symbols to residues. Note: to change the conformation of the selected residue fragment, according to a desired secondary string, use the ICM -object and the set command applied to both sequences and molecular objects.

 
 nice "1est"       # notice that many loops look like beta-strands 
 assign sstructure # now the problem is fixed 
 cool a_ 

assign sstructure segment [ ms_molecules ] # ms_ICMmoleculesPreferable
create simplified description of protein topology (referred to as segment representation). Segments shorter than segMinLength are ignored. The current object is the default. This command will work both on un converted pdb files as well as the pdb files. However the resulting secondary structure will be BETTER when the structure is converted and hydrogens are added.
See also show segment, ribbonStyle, display ribbon. convert convertObject

[ assign residue ]

 
   for i = 1, 8 
     print "Now i = ", i, "and it goes up" 
     if (i == 4) then 
       print "... but at i=4 it breaks, Ouch!" 
       break 
     endif 
  endfor 

Assigns residue structure to a peptide or a protein. Sometimes when you read a peptide or protein from MOL or MOL2 with no residue information present it is treated as a single residue small molecule. This command allows to restore residue layer.

assign residue os1

Example:

build string "EACARVAAACEAAARQ"
read mol Chemical( a_ exact hydrogen )  name="xxx"  # read it as a single residue small molecule
assign residue a_   # restore residue structure
Sequence( a_1. )
Sequence( a_2. )

build

[ Build atom | Build column | Build conf | Build sequence | build tautomer | Build model | Build loop | Build smiles | Build string | Build hydrogen | Build molcart ]

• from sequence file ( build s_seqfile )
• from sequence string ( build string)
• from a linear chemical notation ( build smiles )
• from a sequence and a template by homology ( build model )

build atom as1 [simple] [s_elementName=("c")] [i_bondType=(1)]

build pseudo as_inICMobj
by default it will add a carbon to the selected atom in a non-ICM object and rebuild hydrogens for the affected atoms. Use the strip command for ICM objects.

Options and arguments:

• simple does not rebuild hydrogens.
• s_elementName is a string with the name of the chemical element.
• i_bondType is 1 for a single bond (the default), 2 for a double bond and 4 for a triple bond.

Example:

build smiles "CC(C)Cc1ccc(cc1)C(C)C([O-])=O" name="ibuprofen"
strip a_ibuprofen.
build atom a_ibuprofen.m//c1 "n"
build atom a_ibuprofen.m//c1 2

See also:

• make bond
• delete bond
• delete atom

build column T.col|T

Rebuilds all values in a dependent column T.col

build column T | T_row_selection

Rebuilds all dependent columns in the table T_ or row selection (e.g. T[12], or T.ID==123 ) If column A depends on column B and column B depends on other columns, column B will be calculated before column A.

Examples:

add column T {2 5 1} name="B"
add column T function="A + B" name="C"
add column T function="C + B" index=1 name="D"
T.A[1] = 10
build column T[1] # should change values of C and D in the first row

See also: add column function

Generating low energy conformations for small molecules.

build conf T.mol # requires GINGER license

Building object from sequence file

build s_IcmSeqFileName [ library= { s_libFile | S_libFiles} ] [ delete ]
reads s_IcmSeqFileName.se ICM-sequence file and builds an ICM molecular object. This sequence file is different from a simple sequence file and contains three (sometimes four) character residue names defined in the icm.res residue library file (try show residue types to see the list).

Use command build string if you want to build an object from a string with one letter coded sequences or a named sequence. E.g. build string "ASDGF" or "ASD;DERR" or "nh2 ala his cooh"

To get a D-amino acid instead of L-ones simply use D as a prefix: Dala Darg. Specify N- or C-terminal modifiers directly in the file if needed. The build command will create them in some default conformation (extended backbone with different molecules oriented around the origin as a bunch of flowers). Several molecules can be specified in the ICM sequence file.
Residue names may contain numbers (i.e. 4me ). However, the residue numbers with a modification character, such as 44a, 44b should contain a slash before the modification character (i.e. 44/a , 44/b ). An example in which we create a sequence of residues ala and 4me with numbers 2a and 2b, respectively: "se 2a ala 2b 4me".
The library option lets to temporarily switch the library file. The same result may also be achieved by redefining the LIBRARY.res array of the LIBRARY table.
The delete option temporarily sets the l_confirm flag to no and the old object with the same name gets overwritten. Examples:

 
 build "def"  # def.se file
 build s_icmhome + "alpha.se"  # alpha.se file  
 build "wierd" library="mod.res"  # get residues from mod.res  
# 
 LIBRARY.res = {"icm","./myres"} 
 build "s"  

build tautomer [charge={r_pH,r_window}] ms_het|rs_tautomeric_residues"

prepares internal data for quick switching between different tautomer states of small molecules ms or histidine rs_his by relative tautomer number or histidine tautomer name.

charge option adds enumeration of format charge states at given pH and a window.

You need to call this command if you plan to sample different tautomers in montecarlo command (~~tautomer option)

Example:

build string "AHW"
build tautomer a_/his # adds a hydrogen and hydrogen masks to allow the switching
monecarlo reverse tautomer 

Example:

 build smiles "C(CNN)c1ccccc1"
 build tautomer a_1 charge = {7. 2.}
 set tautomer a_1 1
 set tautomer a_1 2
 set tautomer a_1 3

See also: set tautomer enumerate charge

Building model by homology

[ Homology steps | Loop search | The output ]

Possible modes:
• simple one-to-one mode: build model seq_1 [ms_1] [ali_1]
• N sequences - N corresponding molecules: build model seq_1 seq_2 .. seq_N ms_1,2,..N This mode requires the minimize tether command to complete the construction.

 
 l_autoLink = yes 
 read pdb "x"  
 read alignment "sx"  
 build model ly6 a_  
 ribbonColorStyle = "alignment" # grey-gaps, magenta-insertions 
 display ribbon 

 read pdb "2ins"  # multichain  
 a = Sequence( "GIVEQCCASV CSLYQLENYC N" )
 b = Sequence( "VNQHLCGSHL VEALYLVCGE RGFFYTPKA" )
 c = a
 d = b
 build model  a b c d a_1. 
 minimize v_//V "tz" 1000
# or   minimize tether
# Now optimize the side chains 
 selectMinGrad = 1.5 
 set vrestraint a_/* 
 montecarlo fast v_/!I/x*   
# !It means residues which are not Identical to their template residues 
# use  refineModel to energetically optimize the model 

 
align number a_/* 

 
set vrestraint a_/*  # assigns the rotamer probabilities 
montecarlo fast v_/Cx/x* # x* selects for all chi (xi) angles 

 
set vrestraint a_/*  # assigns the rotamer probabilities 
montecarlo v_/14/x*   
ssearch v_/14/x*     # systematic conformational search for the 14-th sidechain 

The output

The build model command returns the following variables:
LoopTable master table containing list of all the loops, their conformation in alphanumeric code, a measure of the deviation of the database loop ends and the model attachment sites, the loop length and the numerical conformation type (not really important). E.g.

 
#>T LoopTable 
#>-1_Loop------2_Conf------3_Rmsd------4_Nof-------5_Type----- 
   a_ly6.a/7:10 31R21       0.1         11          1           
   a_ly6.a/60:63 1RRR32      0.1         8           1           
   a_ly6.a/43:46 211331RRRR  0.240658    4           1           

 
icm/ly6> LOOP1 
#>T LOOP1 
#>-Conf--------energy------offset------rmsd------- 
   31R21       0.          3623594     0.092104    
   31RR2       1.519275    3427772     0.083372    
   R1121       1.612712    3750108     0.097777    
   R1R32       1.639177    1529882     0.087113    
   R1RR2       1.880638    3806768     0.079335    
   31R32       3.714823    4561270     0.053853    
   R3RR2       4.531406    4003324     0.042881    

 
 read object s_icmhome+"crn" 
 build loop a_/20:26  # rebuild this loop 

build smiles s_smiles_string [ name= s_ObjName]

create an ICM-object from the smiles -string, respectively. Set l_readMolArom to no if you do not want to assign aromatic rings from a pattern of single and double bonds (and formal charge and bond symmetrization for CO2, SO2, NO2or3, PO3 ) upon building. To suppress the symmetrization and consequential charging of CO2, set the l_neutralAcids flag to yes .

Examples:

 
build smiles "CCO"   # ethanol 
 
build smiles "Oc(cc1cc2)ccc1cc2N" 
 
build smiles "Oc(cc1cc2)cc(ccc3)c1c3c2" 

build smiles "C/C=C\C" # cis-2-butene

build smiles "C/C=C/C" # trans-2-butene
 
              # dicoronene 
build smiles "c1c2ccc3ccc4c5c6c(ccc7c6c(c2c35)c2c1c1c3c5c6c"+\ 
             "(c1)ccc1c6c6c(cc1)ccc1ccc(c5c61)cc3c2c7)cc4" 
 
              # NAD 
build smiles "[O-]P(=O)(OCC1OC(C(O)C1O)N1C=2N=CN=C(N)C=2N=C1)"+\ 
             "OP(=O)([O-])OCC1OC(C(O)C1O)N=1C=CC=C(C=1)C(=O)N" 
 
              # Hexabenzo(bc,ef,hi,kl,no,qr)coronene 
build smiles "c1c2c3c4c(ccc3)c3c5c(c6c7c(ccc6)c6c8c(ccc6)c6c9"+\ 
             "c(ccc6)c(cc1)c2c1c9c8c7c5c41)ccc3"  
 
              # rubrene 
build smiles "c1c2c(c3ccccc3)c3c(c(c4ccccc4)c4c(cccc4)c3c3ccccc3)"+\ 
             "c(c2ccc1)c1ccccc1" name="rubrene"

Sometimes the build smiles command is not sufficient. The molecule needs to be optimized in the mmff force field and several conformations need to be sampled. A more rigorous conversion is provided by the convert2Dto3D macro.
See also: Smiles , find molecule.

Building object from string

build string s_IcmSequence [ name= s_ObjName ] [ delete ] [i_first_amino_residue_number (1)]
create an ICM-object from a s_IcmSequence string (see the build command above). To get a D-amino acid instead of L-ones simply use D as a prefix: Dala Darg. Specify N- or C-terminal modifiers directly in the file if needed. The build command will create them in some default conformation.

The build string command also understands short one line version of the full format. The short format looks like "ASD" or "ala his" and may not start from "ml " or "se ".

The possibilities are the following:

• one letter code, - it needs to be specified in upper case letters, e.g. "DD";
• full three-four letter code, e.gg. "nter ala hise Dala cooh"
• multiple molecules - just use a comma, a semicolon or a dot as a separator, e.g. "WWWW;AAAA;EEE" or "ala his trp; nh3+ gly coo-"
• mixed one-letter and three letter code, e.g. "AST-sep-tpo-AAA" to include phosphoserine and phosphothreonine

If the sequence is provided as one letter code (e.g. "ACDTCAA") or as an icm sequence the residue number of the first aminoacid will be set to 1 unless redefined by the optional integer i_first_amino_residue_number.The N-terminal residue "nh3+" will then get number 0.

Option delete temporarily sets the l_confirm flag to no and the old object with the same name gets overwritten.
Examples:

 
   build string "ADG-sep-HRTE" # the charged terminal groups will be added, note phosphoserine
   build string "ADGHRTE" 2 # assign res number of 2 to 1st alanine
   build string "ADGH;RTE" # two peptides, a and b 
   build string "nter ala Dhis cooh" name="pep"  # one peptide named a_pep. 
   build string "ml a \nse nh3+ his coo- \nml b \nse trp" # molecules a and b  
   build string IcmSequence("GHFDSFSDRT","nter","cooh") # translate and add termini 
# 
# Using alias  BS   build string "se $0" 
   BS ala his trp   

Building hydrogens according to topology and formal charges.

build hydrogen [ as_heavyAtoms ] [ i_forcedNofHydrogens ] [cartesian]
adds hydrogens to the specified heavy atoms according to their type and formal charge. All heavy atoms of the current object are used by default. If your have hydrogens already and their configuration is wrong, you can delete them with the delete hydrogen command. The number of hydrogens may be enforced if the optional i_forcedNofHydrogens argument is specified.

Option cartesian means that no new hydrogens are added, but, rather, the existing ones are set to new coordinates according to the heavy atoms (a better syntax for this action is set hydrogen ).

See also the set bond type command, set hydrogen .
Examples:

 
  read mol s_icmhome+ "ex_mol"  # several small molecules  
  display a_4. 
  build hydrogen a_4.  # added and displayed  
#  
  undisplay
  display a_3.
  build hydrogen a_3.
# move one of the nydrogens  
  build hydrogen a_3. cartesian # should put the hydrogen back at a correct position

Building molcart indices for substructure, similarity or exact search

build molcart {s_tableName|S_tableNames} [sstructure|similarity|exact]

builds (or rebuilds) various keys for molcart table.

call

call s_ScriptFileName [ only ]
invokes and executes an ICM-script file. End the script with the quit command, unless you want to continue to work interactively, or use it in other script.
The option only allows one to suppress opening the script file if the call command is inside a block which is not executed. By default the script file is opened and loaded into the ICM history stack anyway, but the commands from the file are not executed.
The absolute path of the script can be obtained by calling the Path ( last ) function.
Example:

 
  call _startup             # execute commands from _startup file  
  show Path( last )

if Type( CONSENSUS ) != "table" then
 call _startup only # only means do not read if the table is already loaded
endif

• only : do not rescale, translate only, i.e. move the selected atoms to the center of the graphics window
• static : scale only according to the visible X-Y dimensions and the margin. Do not take the Z-dimension into account in the size calculation as if you do not intend to rotate objects. That implies an assumption that the orientation of molecules/grobs/maps will not be changed.
• plane : center plane uses GRAPHICS.clippingPlane parameter and has additional options, see below

 
   nice "1est" 
   center                        
   center Sphere ( a_/15:18 )    
   center a_/1:2 only  # keep the scale 
 
   read grob s_icmhome+"beethoven" # a genius  
   display beethoven smooth 
   center beethoven static   # 10 A margin 

center plane foreground|background

command to set clipping planes by resetting four compounds of the GRAPHICS.clippingPlane variable. Make sure to set GRAPHICS.clipStatic to yes.

[ clear-error ]

clear terminal screen
clear selection clear the graphical selection as_graph

Example:

nice "1crn"
as_graph = a_/1:5 # select five residues
clear selection # nothing again

clear pattern chemarray

clear SMARTS search attributes in the input chemical array.

Example:

add column t Chemical("[C;D2]")
clear pattern t.mol   # D2 attribute will be cleared

See also: Exist pattern

clear graphic [ os ] clears display properties , graphic representation memory and reset the graphic planes to the default.

clear error

clears all error and warning bits previously set by ICM. See also Error ( i_code )

[ Color specification | Color object ]

color all|{wire|xstick|cpk|surface|skin|[residue|atom|variable|string] label|ribbon [base]} color as [full]

color as|rs|ms {molecule|object|alignment | R_values [window=R2_fromTo] } [full] [all]

color background|volume color # volume for the depthcuing fog color

color chemical X_chemarray {P_predictiveModel | pharmacophore }

color site ms1 index=i_site|I_sites color_spec

color distance|hbond|angle|torsion P_distParray color

color g accessibility r_depth ([0:1]) # occlusion coloring

color g [add|pseudo] color as GROB.atomColorRadius= r

color g map [m_valuesForColoringGrob]

color g|grob potential [ fast ] [ reverse | simple ] [ms_sourceAtoms] # electrostatic coloring

color map_Name [ I_colorTransferFunction ] [ R2_fromTo ] [ auto ]

Options:

• full : allows one to set colors for atoms that are not displayed in addition to the displayed ones. The default only changes colors of the atoms visible in a given representation. (this option has been added in versions compiled after Sep 15, 2009). This option replaces the set color command for batch coloring.
• all : colors all graphical representations (by default it colors only the specified ones)

To change some of the color defaults permanently edit icm.clr file or these preferences (you may change preferences via GUI or directly in session or user_startup ):

• COLOR.bg
• COLOR.distanceAtom
• COLOR.labelAtom
• COLOR.labelResidue
• COLOR.labelSite
• COLOR.labelVar

See also: set color to set atom or residue color directly and without graphics. See also: icm.clr for allowed color names and their r,g,b values; the plot command needs ICM colors , an sarray can be returned with the Color( R ) command.

Specifying colors in ICM

There are various ways to specify a color in ICM: by name, index or RGB representation.

color_name | color[i_index] | i_Color | r_Color | rgb=rgb_color

Specifying color by name:

color red

Requesting contrasting colors by index:

color color[4]

Example:

  read pdb "1crn"
  display ribbon a_1crn.
  show colors 
  color a_/1:5/* color[89] 
  for i=1,Nof(a_/*) 
    color a_/$i color[i]       # speckled coloring 
  endfor 

color 3

Color indices are taken from the "rainbow" section of the icm.clr file. Currently there are 128 colors (i=0,127) in this section and they form a smooth transition from blue to red via white (not really a rainbow). You may change the "rainbow" colors in the icm.clr file. Number 128 becomes blue again. Using integer color indices is convenient for automatic coloring within ICM loops.

Example:

 
   display "Colors" 
   for i=1,255 
     color background i 
     print i 
   endfor 

Specifying colors interpolated between indexed colors:

color 4.5 

The color 4.5 will be the average between the "rainbow color" 4 and "rainbow color" 5.
Specifying colors by their RGB representation

Color is defined as a combination of red, green and blue components. The triple may be specified in different formats:

rgb = R_3rgb

- as an array of 3 reals in 0..1 range

rgb = I_3rgb

- as an array of 3 integers in 0..255 range

rgb = s_#rrggbb

- as a string where each component is defined by two characters in hexadecimal form. Optionally prefixed with a hash symbol ("#").

Examples setting magenta color (mixture of red and blue):

color rgb={255,0,255}
color rgb={1.,0.,1.}
color rgb="#ff00ff"
color rgb="ff00ff"

In case the requested RGB color is not available for the graphics system, ICM finds the closest color.

Coloring molecular objects

The main color command:
color [ as ] graphic_representation [ color_spec ]

color [ as ] graphic_representation [ I_colors | R_colors ] [window = R_2MinMax]

graphic_representation, when specified, must be one of the following

wire | hbond | cpk | ball | stick | xstick | surface | skin | site | ribbon [base]

This command colors selected atoms ( as_ ) or graphics object(s) according to the specified color. It is possible to either specify a single color color_spec, or provide an array ( rarray or iarray ) of colors to color each element of the selection according to a certain property, as electric charge or Bfactor.

The scale is determined by the minimal and the maximal elements of the array, independently of the array length. First the numbers in the array are scaled so that its minimum corresponds to the first color in the "rainbow" section and its maximum to the last color. Then the scaled numbers are applied sequentially to the elements of the selection. If the number of elements in the array is shorter than the number of elements in the selection, the array is applied periodically. If the color array is longer than the selection, the excessive numbers are not used for coloring but (attention!) they will be used for scaling.

The window={ minValue, maxValue } option allows one to provide a range for color mapping. It will be used instead of the array minimum-maximum value range as the range from which the color array elements will be mapped into the rainbow colors. Moreover, values in the color array will be clamped to be in the window range.

In the following example the Bfactor(a_/ simple) values which may range from large negative values to large values will be clamped to the [4.,40.] range.

  nice "1ekg"
  color ribbon a_/ Bfactor(a_/ simple) window=4.//40.

 
  read object s_icmhome+"crn"
  display a_crn.
  color a_//* Charge(a_//*) window={-1.,1.}

It is also possible to show a color bar in the graphics window by changing the GRAPHICS.rainbowBarStyle property.

Each of the command arguments has a default:

• objects as_: the current object ( a_ ) only. Hint: to color all objects, use a_* .
• graphic_representation: all except ribbon. Ribbons should be colored explicitly using a color ribbon command.
• color_spec. The default coloring is by atom type, except for the ribbon representation which is colored by secondary structure by default.

In DNA and RNA ribbons, bases can be colored separately (e.g. color ribbon base a_1/* white ), the default coloring being A-red, C-cyan, G-blue, T or U-gold.

Examples of how the defaults work:

 
 nice "1crn" 
 display       # also displays wire 
 color         # all except ribbon colored by atom type 
 color ribbon  # only ribbon of a_ by secondary structure type  
 color ribbon red         # only ribbon as specified 
 color a_/1:10 ribbon yellow # parts

More examples:

 
 build string "ASDWER"     # hexapeptide 
 display
 color a_/1:4 green    # the first four residues in green  
 color                 # return to default colors by atom type  

 
 read pdb "1crn"
 display a_1crn. only 
                       # color atoms according to their B-factor  
 color a_1crn.//* Bfactor(a_1crn.//*) 
                       # crambin's ribbon  
                       # from blue N-term to red C-term gradually  
 display a_/* ribbon only 
 color a_/* Rarray(Count(1 Nof(a_/* ))) ribbon 
 
                       # another crambin's ribbon  
                       # from blue N-term to red C-term gradually  
                       # thick worm representation 
 assign sstructure a_/* "_"  
 GRAPHICS.wormRadius= 0.9 
 display a_/* ribbon only 
 color a_/* Count(1 Nof(a_/* )) ribbon 

Coloring 2D molecules in a chemical table

color chemical X_chemarray P_model

calculates atom contributions to the total value calculated by the P_model if this model is

• linear. (PLS)
• built using counted fingerprints (no external column-descriptors)

color chemical X_chemarray pharmacophore

color by built-in pharmacophoric definitions The list of definitions can be listed like this:

icm/def> show pharmacophore type
name         codesmarts                        color
-------------------------------------------------------
Negative     [Qn]C(~[O;D1])~[O;D1]             #87cefa
Negative     [Qn]P(~[O;D1])(~[O;D1])(~[O;D1])~*#87cefa
Negative     [Qn]S(~[O;D1])(~[O;D1])(~*)~*     #87cefa
Positive     [Qp][N;D3;$(N(-[*;^3])(-[*;^3])-[*;^3])]#fa8072
Positive     [Qp][N;D2;$(N(-[*;^3])-[*;^3])]   #fa8072
Positive     [Qp][N;D1;$(N-[*;^3])]            #fa8072
Positive     [Qp]C(~[N;D1])~[N;D1]             #fa8072
HBA          [Qa][O,S&v2,N&^2&X2,N&^1&X1,N&^3&X3]#98fb98
HBD          [Qd][!C;!H0]                      #ee82ee
Aromatic     [Qm]a                             #ffa500
Hydrophobic   [Qh][C&!$(C=O)&!$(C#N),S&^3,#17,#15,#35,#53]#e0ffff

How to color grob surface by depth

[ Color molecule | color background | color by alignment | color grob | color label | color map | color volume ]

color accessibility g_mesh [ r_maxShade ]

modify the color of each surface element of a grob to create perception of depth. The procedure calculates for each surface element (triangle) the extent it is occluded from ambient light by other parts of the molecule, and makes the elements darker proportionally to occlusion. Thus, concave regions such as pockets become dark since the surrounding bulk of the protein blocks the light from most directions, while protrusions remain bright since they are well exposed. Repeated application of the command or using a larger r_maxShade (the default is 0.8) generates a more dramatic shading of the shape.

Example:

color accessibility g_electro 0.7
color accessibility g_electro 0.7 # do it two times for a more dramatic effect

  clrs = Color(g_electro)
  # change grob color, e.g. with color accessibility
  color grob clrs

Uniquely coloring by object, molecule, residue or atom

color graphic_representation [ as_molecules ] [object|molecule|residue|atom]
a special command to color the displayed and selected molecules differently. The graphic representation field can be either empty, or one of those: wire xstick cpk surface skin ribbon, residue label, atom label, site label, variable label . E.g. select graphically some atoms and do this:

color xstick as_graph & a_*.//c* molecule  
color ribbon as_graph object
color cpk as_graph molecule
color residue label as_graph residue

sets the background to the specified color color_spec in one of the supported formats .

Examples:

color background blue 
color background lightyellow
color background rgb={255,255,255} # white. integers in 0..255 range
color background rgb={0.,1.,0.} # green. reals in 0.. range

See also: COLOR.bg , rgb, color background example .

• residue type
• consensus character at the residue position in the alignment
• colors as provided by the CONSENSUSCOLOR.tabtable.

 
  read sequence s_icmhome+"sh3" 
  nice "1fyn" 
  make sequence a_1  # extract 1st sequence 
  group sequence sh3 
  align sh3 
   
  color a_1 ribbon alignment 
  display skin white a_1 molecule
  color a_1 alignment   # colors all representations including skin 

color grob

[ Color grob unique | Color grob matrix | Color grob by atom selection | Color grob map | Color grob potential ]

Color is a powerful mechanism of showing extra information on ICM grobs ICM grobs may have individual colors assigned to each vertex, which allows one to use grob coloring to illustrate properties of 3D surfaces.

The simplest way to set grob color is to paint it to a single color.

color g_grobName color_spec

colors the whole g_grobName grob to the color_spec color.

color grob color_spec

colors all grobs to color_spec.

Check out the color specification section for available color_spec options.

Example:

torus = Grob("TORUS",3.,1.)
display torus
color torus black # paint it black
color background white # this should improve the visibility
color torus rgb={127,255,212} # aquamarine, as some people call it

Automatic assignment of different colors to different grobs

color grob unique
In addition to the main color command which colors grobs there is a special command to automatically assign the displayed grobs to different colors.

See example for the split grob command.

Coloring grob by matrix of RGB values for each vertex.

color g_grob M_rgbMatrix
allows one to set individual colors to grob vertexes. Colors are specified in RGB format in the M_rgbMatrix.Each row of the matrix is an RGB triple. This type of matrix may be obtained by the Color( g_grob ) function.

Examples:

torus = Grob("TORUS",3.5,0.5)
display torus smooth
n = Nof(torus)
R_rgb = Count(1 n/2)/Real(n/2) // Count(n-n/2 1)/Real(n-n/2)
add matrix M_rgb R_rgb
add matrix M_rgb Rarray(n,0.3)
add matrix M_rgb Rarray(n,0.7)
color torus Transpose(M_rgb)

This command allows one to create special effects, like gradual disappearance of a grob into background:

# set the scene
color background black

# uncomment these lines to get a more sophisticated example
# torus = Grob("TORUS",3.5,0.5)
# display torus smooth 
# color torus blue

# the active grob
g = Grob("SPHERE",3.,5)  # a wire sphere  
display g smooth 
color g Random(Nof(g),3, 0., 1.) # color randomly 
M_colors = Color(g)               # extract current colors 
# make the sphere disappear (modern poetry)  
for i=1,20    # shineStyle = "color" makes it disappear completely 
 color g (1.-i/20.)*M_colors  
endfor         
for i=20,1,-1 # bring the sphere back  
 color g (1.-i/20.)*M_colors  
endfor 

color g_grobName as_closeAtoms color_spec [add|pseudo]

color g_grobName M_xyz distance color_spec

colors vertices of the grob which are less than GROB.atomSphereRadius to any of the selected atoms or XYZ coordinates. The default value for the radius is 4Å.

Options:

• add : adds van der Waals radius for each atom to the GROB.atomSphereRadius parameter
• pseudo : for hydrogen bonding acceptors considers distances from LONE-PAIR centers at 1.7A distance from the acceptor atoms. If an atom is not an acceptor, the atom itself is considered. Note that a_//HA is a selection for hydrogen bonding acceptors and a_//HD is the donor selection.

Example in which we color 1.3 radius sphere around the lone pairs of hydrogen bonding acceptors:

color a_REC.//HA g_pocket magenta pseudo  GROB.atomSphereRadius=1.3

See color specification for the definition of color_spec.
See also: Grob( g R_6) function to return a patch of certain color.

Example:

nice "1crn"
make grob skin a_1crn. name="g_1crn"
display g_1crn
color g_1crn green
color g_1crn a_1crn.//1:60 red # color a patch by atom proximity

See also: make grob skin, make grob potential .

Coloring surfaces by 3D scalar field

color g_grob map map_Name I_transferFunction R_2mapValueBounds [ color_spec ]
colors vertices of the g_grob by the values of the map_Name . The map values at each grid point are first clamped into the R_2mapValueBounds range, then this range is divided according to the number of elements in the transfer function and each point is colored according to the value of the transfer function. The optional color_spec parameter is explained in the color specification section.
The new color will be mixed with the current color of grob points. Therefore if you want to color each of 3 RGB channels with a different normalized property value, first color the grob black, and then color with the red , green , or blue color depending on which channel you intend to use. Note that zero in the transfer function correspond to no color . Corresponding grob nodes will not be colored.
Transfer function is the same to the one in color map but has certain differences. This function (e.g. {0 0 0 1 2 3} ) contains any number of positive integers. 0 means "do not color", and each positive value is a scaling factor for the color provided as an argument, or a parameter to select a color from a predefined rainbow. In the above example, the R_2mapValueBounds range will be divided into 6 ranges and each value range will be colored accordingly.
Example in which we color the vertices of a grob by inverted values of truncated hydrophobic potential:

 
  read obj s_icmhome+"data/xpdb/1sre.ob"
  display a_	
  make grob skin a_2 a_2 name="g_pocket"        # create g_pocket 
  make map potential "gs" Sphere( g_pocket a_1) 
  compress g_pocket 1. 
  color g_pocket black 
  color g_pocket map -m_gs { 0,0,0,3,4,5 } { 0. 0.5  } green           
  display g_pocket
  h = Transpose( Color( g_pocket ) )[2]  # extract hydrophobicity 

Coloring grob by electrostatic potential

color g|grob potential [ fast ] [ reverse | simple | heavy ] [ms_sourceAtoms]

(REBEL feature) calculates electrostatic potential waterRadius away from the surface of the g_skin graphics object and color surface elements according to this potential from red to blue. Important the location of the center of the water probe is determined by the grob normal ( you can change it with the set g_ reverse command). If you compute the potential at a blob outside the molecule but with the normals point outwards, use the reverse option. To compute potential without any positional correction including normals use the simple option. The potential is calculated either by the REBEL boundary element solution of the Poisson equation, or, if option fast is specified, by a simple Coulomb formula with the dielConstExtern dielectric constant (78.5 by default). The calculation is also affected by the TOOLS.rebelPatchSize parameter (1. by default), and option heavy . Option heavy is preferred.

The local value of potential is clamped to the range [ -maxColorPotential, +maxColorPotential ]. It means that a potential larger than maxColorPotential is represented by the same blue color, while values smaller than maxColorPotential are represented by the same red color. The real range is reported by the command and you can adjust maxColorPotential to cover the whole range. To suppress the absolute maxColorPotential threshold and use auto-scaling instead set maxColorPotential to 0. The color bar with values will appear according to the GRAPHICS.rainbowBarStyle preference. There are two macros to generate potential-colored skins: rebel and rebelAllAtom
The second one (given below) considers all the atoms (including hydrogens) with their charges.
The mean value of the potential at the surface is returned in r_out , and the root mean square deviation of the potential is return in r_2out shell variables, respectively. The averaging is free from bias due to uneven density of grob points. It uses equal size cubes distributed evenly over the surface. The number of representative cubes used for the calculation is return in i_out .

Examples:

 
read object s_icmhome + "crn"
display a_1
make grob skin a_1 name="g_crn"
make boundary a_1
display g_crn
color g_crn potential

color label as [ I_colors | R_colors ]
Colors labels associated with the selected residues or atoms. A simple option is to specify a single color using color specification formats. It is also possible to provide colors for each atom using an iarray I_colors or rarray R_colorsIf no atom selection is specified, all labels are colored.
Examples:

 
 read object s_icmhome + "crn" 
 display a_//n,ca,c white 
 display label residue 
 color label a_/* Count(1 Nof(a_/*)) 
 #
 color label a_/5:10 magenta 

 read object s_icmhome + "crn" 
 display a_//n,ca,c white 
 display label residue 
 color label lightyellow 

color map_Name [ I_colorTransferFunction ] [ R2_fromTo ] [ auto ]
color the current or the specified map according to the color transfer function supplied as I_colorTransferFunction.
The default: By default the maps are colored in such a way that points with zero map values become transparent while values above and below zero are colored by shades of blue or red, respectively.
The R2_fromTo array of two elements allows one to set the lower and the upper boundaries for the red and blue colors, respectively. All values above and below will be trimmed to the range. For electrostatic maps the array is set to -5.,5. by default.
In the auto mode all grid points are divided to Nof( I_colorTransferFunction ) color classes according to the normalized function value (sigma units around the mean value) and each class is colored as specified in the I_colorTransferFunction (0 means transparent).
If the number of I_colorTransferFunction elements is odd (2* n+1 ) the class boundaries are the following:

• -infinity
• Mean- n *sigma,
• Mean-( n -1)*sigma,
• Mean-( n -2)*sigma,
• ...
• Mean- 1*sigma,
• Mean
• Mean+ 1*sigma,
• ...
• Mean+( n -1)*sigma,
• Mean+( n )*sigma.
• +infinity

• {0 0 0 0 0,0 0 0 3 10} default map coloring, color only high densities (blue from 3 to 4 Sigma, red >4 Sigma). Comma only shows you where the mean is.
• {0 1 0} color only Mean+- 0.5*sigma nodes, ignore high and low densities.
• {1 0 2} color low and high densities by different colors, ignore densities around the mean.
• {1 2 3 0 5 6 7} similar the previous one, but with more grades

read pdb "1crn"
make map potential name="mpot"
color mpot {1 2 0 4 5}
# OR
color mpot

color volume color_spec

determines the color of the fog in the depth-cueing mode ( activated with Ctrl-D ). Format of color_spec is explained here.

For example, if you want that distant parts of you structure are darker (black fog), but the background is sky-blue, you will do the following:

 
color background lightblue   
color volume black  

[ Compare atom | Compare variables | Compare surface ]

sets a metric for calculating a distance between different conformations in a stack .
The goal of the two following compare commands is to provide a desired setting before the montecarlo command and stack operations. This command defines a filter which is used to decide how many and what conformations from the stochastic optimization trajectory are kept as low energy representatives of a certain area in conformational space. This metric is also used for the subsequent stack manipulations, e.g. compress stack.
The compare command defines the distance measure between molecular conformations which is used to form a set of different low energy conformers in the course of the stochastic global optimization procedure. The defined distance is compared with the vicinity parameter and determines whether two conformations should be considered different or similar (i.e. belonging to the same slot in the conformational stack). The compare command determines the spectrum of conformations that will be retained in the stack, accumulated during a montecarlo procedure. The default comparison set is a set of all free torsion variables (see compare vs_ ). Other methods compare atom RMSD with and without superposition, using chemical superposition, and compare only the atoms in the interface with a molecule ( compare surface ).

Please note that the compare command can change the compareMethod preference. Example:

  montecarlo v_//2 compareMethod ="chemical static"  # suitable for docking

See also montecarlo, compareMethod
Unrelated array comparison tools:

• Index( compare)
• Distance

 
   compare v_//phi,psi            # compare ONLY the backbone angles  
   vicinity=30.0                  # consider two conformations  
                                  # with phi-psi RMSD < 30. as similar  
 
   compare a_2//ca static         # compare Cartesian deviations  
                                  # of the second molecule's alpha-carbon atoms  
                                  # without prior optimal superposition  
   vicinity=3.0                   # consider two conformations with second  
                                  # molecule deviation < 3 A as similar  

compare surface as_currentObjSelection | as_staticReferenceObject.
Similarly to compare static as_ it will look at absolute deviations of coordinates, but the comparison will be applied dynamically only to a patch sub-selection of the atoms in the current object in the selectSphereRadius (default 5. A) proximity to the non-current-object atoms of the as_ selection. The selection typically would look like this: a_activeIcmObject.//ca | a_staticPdbReceptorObject.//ca
Example:

 
 compare a_runObj.//ca | a_recName.//ca surface 

 
 read pdb "1bgs"     # a complex 
 read pdb "1a19.a/"  # the protein ligand only 
 convert  
...     # make maps and other actions to prepare protein-protein docking 
 compare a_//c* | a_1.1 surface  # will use only  
 selectSphereRadius = 7. 
... 
 montecarlo  

[ Compress alignment | Compress grob | Compress stack | Compress binary ]

compress ali

removes gapped columns in place.

compress graphical objects

compress g_grobName1 g_grobName2 .. [ r_minimalEdgeLength=.5 ]

compress grob [ selection ] [ r_minimalEdgeLength=.5 ]
simplify a grob (graphical object) by eliminating/merging small triangles into bigger ones. This procedure allows one to generate very "low-resolution" molecular surfaces. The default value of the r_minimalEdgeLength is 0.5 Angstroms. Typically compression with the 1. A minimal edge parameter reduces the number of triangles by an order of magnitude. The compression algorithm does not change the connectivity of the surface. Therefore you can still split the compressed grob and find the fully enclosed cavities.
The compress command returns the new number of verteces in i_out and the new number of triangles in r_out variables, respectively (for the last compressed grob only).
Example:

 
read pdb "1crn" 
make grob skin smooth name="g_1crn" # creates a grob with many triangles 
display g_1crn 
compress g_1crn 1. # significantly reduces the number of triangles in the grob
display g_1crn 
compress g_1crn 4. # further simplification of the grob
display g_1crn 

See also:

• delete all compress # to delete all objects/grobs/maps not used in slides
• compress binary file.icb # compresses .icb file files

compress stack [ fast ] [ i_fromConfNumber i_toConfNumber ] [r_enerDiff]

compress stack tree [number=nClusters]

regular compression Remove similar and/or high energy conformations from the conformational stack. During a montecarlo run, some conformations of the generated conformational stack may be substituted by newly calculated ones with lower energies. New conformations may violate the initially correct distribution of the conformations in the slots of the stack as defined by the vicinity parameter and by comparison mode specified by the compare command. The compress command compares all the pairs of the stack conformations, identifies pairs of conformations in which two conformations are separated by a distance less than the vicinity threshold, and removes the higher energy stack conformation from each close pair. Optional arguments i_fromConfNumber and i_toConfNumber define a subset of the conformations in the stack which are to be analyzed and compressed (if any). The whole stack (from the first to the last conformations) is processed by default.
Note that if two close conformations are compressed into the better energy one, the number of visits of the resulting conformation will be a sum of the two numbers of visits.
The fast option applies an iterative compression algorithm which can be several orders of magnitude faster but the result may slightly differ form the default compress. The fast algorithm algorithm performs the following steps:

1. sort conformations by energy
2. start from the lowest energy conformation
3. find all conformations with higher energy than the current conformation within vicinity .
4. delete similar conformations with higher energies and compress stack
5. move to the next conformation in the new sorted stack, make it current and go back to step 3

 
 build string "VTLFVALY" 
 mncallsMC = 5000 
 montecarlo   # generates stack
 write stack "f1" 
 delete stack # clean up and 
 montecarlo   # generates another stack 
 read stack append "f1"  #  
 compare v_/2:5/phi,psi  # compare settings are different 
 vicinity = 40.          #  
 compress stack fast 
 vicinity = 20.          # new vicinity 
 compress stack  
 compress stack  2.0  # remove confs > 2 kcal/mole higher than the lowest one

compress stack tree (only for the compareMethod = "atoms static" )

The algorithm with the tree option performs clustering of conformations based on either vicinity parameter (adaptive n_clusters, the number of clusters may vary) or an explicit number= n argument that defines the number of clusters (adaptive vicinity threshold). One representative with the lowest energy is picked from each cluster.

Example:

#generate a large stack
  compare static a_//c,ca,n,o,cb  # applies compareMethod = 2 inside 
  vicinity = 2.
  compress stack tree  # first pass to reduce to 'one-per-cluster'
  if(Nof(conf)>100) compress stack tree number=100

See also: compress binary

compress binary s_inputfile [ filename=s_gzipfile | delete ]

Compresses the s_inputfile file using GZIP algorithm. If the filename is specified, the compressed file will be saved as s_gzipfile.If the delete option is specifeid, the compressed file replaces the input file (in place compression). Otherwise (by default) .gz extension is added to produce the compressed file name.

Example:

read pdb "1crn"; make map potential name="x"; write map x # create x.map file

compress binary "x.map" delete # compress in place

See also:

• delete sequence compress
• delete all compress # leave only objects in slides
• compress grob

connect

[ Connect molcart ]

connect none

connects selected molecules to the mouse for independent rotation (by the LeftMouseButton) and translation (MiddleMouseButton) with respect to the original coordinate frame.

Option append will add selected molecule to the previously connected molecules
Note, that rotations/translations in the connect mode actually change the atomic coordinates of the selected molecules and keep the coordinate system unchanged in your graphics window.
To restore the usual global mode (i.e. all objects/molecules are disconnected and the mouse does not change their absolute positions, but rather the point of view), hit the Esc key when the cursor is in the graphics window. To restore the global mode temporarily press the Shift button.
Use: connect none to switch back to the global connection Examples:

read pdb "1eff"
copy a_1eff. # create something else in the scene
display ribbon a_*.
connect a_1eff.
# move it around now
connect none # disconnect

connect molcart {S_host_user_pass_db|s_host s_user s_pass s_db} [name=s_connectionID]

Connects to the database server specified by the command parameters. It is possible to also specify the s_connectionID which will be assigned to the connection. Parameters returned by the Name(sql connect) may be used in this command.

connect molcart on

Reconnects to the current Molcart.

connect molcart refresh

Reconnects to Molcart using settings stored in user's preferences.

connect molcart filename=s_file [s_db] [name=s_connectionID]

Opens a Molsoft database file. Database name s_db and the s_connectionID may be specified.

connect molcart s_connectionID off

Disconnects specified Molcart connection. See molcart connection options for explanation

connect molcart local off

Closes all open database files.

See also: molcart, molcart connection options, list molcart, set molcart, Name molcart.

continue

continue

skip commands until the nearest endfor or endwhile .
Example:

 
for i=1,5 
  if i==3 continue  # do not print 3 
  print i 
endfor 

[ Convert comp | Convert fragments | Convert mol | Convert and reroot ]

convert as_icmRootAtom [sstructure=as_scaffold] [auto] # root the icm-tree at as

convert rs_patches ..
the first convert command converts an incomplete non-ICM-object (e.g. object of type 'X-Ray' resulting from the read pdb command) into a true ICM-object for which you may calculate energy, build a molecular surface and perform all operations.

Options:

• auto - convert in place, preserve graphics and selections, e.g. convert auto selftether
• charge - transfer charge from the original
• exact - do not use the icm.res library by res name, convert as is.
• heavy - regularization (obsolete)
• graphic - transfer graphical attributes
• selection - transfer selection (as_graph)
• simple - special mode for disjoint chemicals
• tether - impose tethers to the original (use selftether for in-place or auto mode)
• tree= s_smiles - build the tree according to the smiles topology (small mol. convertion)
• selftether - imposes selftethers to the original coordinates, set field for the added heavy atoms ("_ADDED") and shifted upon conversion atoms ("_SHIFTED"), e.g. display cpk Select( a_// "_ADDED")

Description
There are two principally different modes of conversion. In the default mode the program looks at the residue name and tries to find a full-atom description of this residue in the icm.res file. This search is suppressed with the exact option.
Hydrogen atoms will be added if the converted residues are known to the program and described in the icm.res library. If the object selection is omitted, the current object will be converted. If default s_newObjectName is generated by adding number "1" to the source object name. If s_newObjectName is the same as a name of the input object, the input object will be overwritten. (in-place conversion)

The default convert command is best used to convert PDB entries which have explicit residue descriptions and usually do not have hydrogen coordinates. In this mode each residue name is searched in the icm.res file and the coordinates of the present heavy atoms are used to calculate the internal geometrical variables (bond lengths, bond angles, phase and torsion angles) for the full atom model.

Every ICM atom will store the original coordinates as selftether (try show a_// and watch for the ts= x , y , z record. Later these selftethers can be used with the "ts" term.
The exact option: converting protein with unusual amino-acids
Some pdb-entries may contain non-amino acid residues, or modified amino-acid residues which do not need to be replaced by standard full atom library entries with the same name . In this case use the exact option. This option suppresses interpretation by short residue name and converts the existing atoms and bonds in single-residue molecules (amino acids in peptides and proteins will still be extended by hydrogens upon conversion, to suppress that conversion write the molecule as mol and read it back, then convert exact ). Option exact may be necessary because chemical compounds with a four-letter short name identical to one of the amino-acid residues, could be mistakenly converted into an amino-acid with a corresponding name.
The charge option
Normally, upon conversion, the atomic charges are taken from the icm.res library entries. Option charge tells the program to inherit atomic charges from the os_non-ICM-object. For small molecules, use set charge, set bond type and, possibly, build hydrogens before conversion of a new compound. i_out will contain the number of heavy atoms missing from the pdb-template.

The graphic option preserves the graphical representations and colors as is.

The selection option preserves the atom selection bit during the conversion. Useful for in-place convert.

The sstructure= tree_substructure option makes sure that the tree is drawn through the substructure. It also needs a consistent entry atom provided as as_newRoot argument.

The auto option converts in-place preserving graphics and selection information. This is a convenient shortcut for the following combination:

• graphic
• selection
• s_newObjectName is set to the input object name

The smiles option ( an addition to auto option ) allows one to explicitly derive a tree structure from the smiles string. If the smiles string matches only part of the molecule then the rest of the tree will be built according to the default rules.

Additional cleanup
Actually more procedures need to be performed to prepare a functional object from crystallographic coordinates, e.g. identifying optimal positions of added polar hydrogens, assigning the most isomeric form of histidine , and finding a correct orientation of side-chain groups for glutamine and asparagine.
We recommend the convertObject macro instead of the plain convert command to achieve those goals.
Refining the model
To refine a model use the refineModel macro.
convertObject macro
The convertObject macro is a convenient next layer on the convert command. The macro may convert only a few molecules out of your pdb file, optimize hydrogens and do some other useful improvements of the model.

Output.

• the converted object
• i_out : the number of heavy atoms missing from the pdb-template,
• r_out : rmsd from the pdb-template atoms (non zero for residues with bad coordinates),
• i_2out : the number of deviating by more than 0.2A atoms heavy atoms,
• r_2out : the maximal deviation

• "built" -heavy atoms that were missing in a pdb (e.g. some lys and arg in 1qz5)
• "shifted" -atoms that shift after conversion (e.g. silly lysines in 1qz5)

Example:

read pdb "1crn"
display
as_graph = a_//c*
convert auto    # converts in-place preservinf slection and graphics
strip virtual
convert         # creates new a_1crn_1. object

If single atom is provided as an input selection it will be taken as a new ICM tree root. See convert and reroot for details.

See also:

• strip
• convertObject
• convert2Dto3D
• set cartesian
• selftether
• Select ( as s_tag )

• uses all-atom residue templates (including hydrogens) from the icm.res library
• creates temporary ICM-library descriptions for unknown residues
• makes geometry identical to the PDB coordinates: bond length and bond angles may be distorted.
• the converted structure will be energy strained because of common imperfections of the PDB entries and the hydrogen atoms added by the procedure
• C-alpha-only structures will not be properly converted because a special prediction algorithm is required to extrapolate the coordinates of all atoms from C-alpha atom positions.
• these objects are good enough for graphics, skin, secondary structure assignment, rigid body docking. They are not good for loop modeling and side-chain modeling.
• needs to be followed by polar hydrogen placement and histidine state prediction ( implemented in the convertObject macro )

• you need to create a sequence file first and use the build command;
• you will need to create the missing residues manually, say, with the write library command;
• build will use all-atom residue templates including hydrogens, and will preserves the fixation;
• the linear chain with fixed idealized covalent geometry or, actually, any fixation you define, will be threaded onto the PDB coordinates in the best possible way;
• Ca-atom PDB structures will be handled properly if all backbone torsion angles are unfixed;
• the resulting ICM-object will be strained and will need further relaxation.

• uses minimize tether to create the starting conformation;
• employs a multi-step energy minimization (annealing) of the structure to relief energy strain;
• these are the best objects that can create in ICM for further simulations.

 
   read pdb "1a28.a/"           # reading just the first molecule 
   convertObject yes yes no no  # the best way to prepare for docking 
                                # convert + optimizes polar H, His and Pro 
 
   read pdb "1crn"         # X-ray object, no hydrogens, no energy parameters  
   convert                 # a_1crn_icm ICM-object will be created  
   convert a_1. "new"      # a_new. ICM-object will be created  
   convert a_1. exact      # keep modified residues as is 
 
   read mol2 s_icmhome+"ex_mol2" 
   set object a_catjuc. 
   build hydrogen  
   set type mmff 
   set charge mmff 
   convert  

If you want to create a local "epitope" of a protein with chain fragments around a particular area, it can be done with the

convert rs_fragments

command. This command will create a molecule divided into fragments and each fragment will start from virtual atoms vt1 and vt2 and will be controlled with 6 virtual variables. The first vt1 of the second, third etc. fragments will be connected to the first real atom of the first fragment. Example:

read pdb "1crn"
convert a_/4:10,12,27:33,41:45
Nof( a_m//vt1 ) # the number of pieces
show v_/P1/V  # the pos. variables of the 1st part
show v_/P2/V  # the pos. variables of the 2st part
display ribbon
color ribbon a_/P3  # showing the 3rd part

This operation is useful to create a local patch object for docking of global optimization.

Converting a chemical compound from a mol/sdf or mol2 files.

To convert a chemical from GUI menus, follow these steps:

• make sure that bond types and formal charges are correct
• select the MolMechanics.ICM-Convert.Chemical menu item, check the parameters and press OK. Normally to convert from 2D to 3D you need to optimize the ligand. ICM will perform a multiple start global optimization using the MMFF94 force field ( internally it runs the convert2Dto3D macro ). If you want to preserve the geometry, select the keepGeometry option.

 
# assuming that bond types and formal charges are correct 
build hydrogen  
set type mmff 
set charge mmff   
randomize a_//!vt* 0.01 # sometimes it helps to avoid singularities 
convert 
set v_//T3 180.  # making flat peptide bonds 
fix v_//T3       # optional 

Example of geometry optimization:

read mol input = String( Chemical("C(C(O)=O)N1C(C(=Cc2ccc(c3ccccc3[Cl])o2)SC1=S)=O"))
convert2Dto3D a_ yes yes yes yes   
list convert2Dto3D

auto option behaves as in normal convert command. It preserves selection and graphics and preforms in-place conversion.

If you need to reroot an ICM object, do the following:

• strip it to a non-ICM object: e.g. strip virtual
• re-root and convert, e.g. convert a_//hb1 .

Example:

build smiles "C(=CC=C(C1)C(=O)O)C=1"
display wire
wireStyle = "tree"
strip a_ virtual
convert a_//h31 auto   # converts from a new root

copy

[ copy-object ]

copy os [ s_newObjectName ] [delete|display|graphic|selection|stack|strip|tether]

creates a copy of os_ with the specified name. Default source object is the current object. The default name is "copy" (object a_copy. )
Options:

• delete forces the command to overwrite the object with the same name if there is a name conflict.
• display or graphic copy the display attributes of the parent
• selection copies named selections defined on the parent object into the copy
• stack copies internal stack of the object (see store-object-stack) (the stored stack is not copied by default)
• strip applies the strip operation to the copied object. The stripped object has a PDB type and is much smaller in memory.
• tether applies tethers from the source object to the atoms of the copy-object. For further refinement see the refineModel macro.

Examples:

 
 read pdb "1crn" 
 copy a_           # creates a_copy.    
 copy a_1. "aaa"   # creates a_aaa.  

 read object s_icmhome+"crn" # read ICM object 
 copy a_ strip delete tether # create a_copy. and tether to it 

 
crypt key="HeyMan" "_secretScript"    # encrypt and create *.e file 
crypt key="HeyMan" "_secretScript.e"  # decrypt it

ss="Secret rumour: Div(Rot(F))=0 !" 
crypt key="fomka" string = ss  # encrypt 
show ss 
crypt key="fomka" string = ss  # decrypt 
show ss 

Date data-type

A basic ICM class for arrays of date objects

See also: Date.

delete ICM shell objects

[ Delete shell object | delete alias | Delete molcart | Delete plot | Delete selection | Delete variable | delete atom | delete directory | delete file | Delete session | delete hydrogen | delete object | delete molecule | delete bond | delete boundary | Delete column table | delete conf | delete drestraint | delete label | Delete label chemical | delete link | delete map | delete sequence | delete site | delete sstructure | Delete site alignment | delete disulfide bond | delete peptide bond | delete stack | Delete stack object | Delete element | delete table | delete term | delete selftether | delete tether | Delete parray | Delete chemical selection ]

delete all # to delete all shell objects not marked with a no delete flag

ICM-shell objects have unique names; to delete some of them just type
delete [ mute ] { icm-shell-objectName1 | s_namePattern1 } icm-shell-objectName2 ...
You may use name patterns with wildcards (see pattern matching) and add explicit specification of the ICM-shell object type, if you want the search to match only the objects of particular type. If the ICM-shell object type is not specified, all the shell-variables will be considered.
Option mute will temporarily switch off the l_confirm flag.
delete class

delete string className

delete string command | html

to delete icm-command files or html-documents loaded into ICM

delete rarray view

to delete all the views (returned by the View() function)

Examples:

 
   delete aaa           # delete ICM-shell object aaa  
   delete a b c         # delete ICM-shell objects a, b and c  
   delete "*"           # delete ALL ICM-shell objects added by user  
   delete "mc?a*" mute  # delete ICM-shell objects matching the pattern  
   delete rarrays       # delete ALL real array  
   delete objects       # delete ALL molecular objects, same as delete a_*.  
   delete rarray "a*"   # delete real arrays starting with 'a'  

 
  a={1 2 3 4 5 6}   # we want to delete elements from it 
  a=a[2:4]          # retain only elements 2:4 
  a={1 2 3 4 5 6}    
  a=a[{2,3}//{5,6}] # retain only 4 elements elements  
  a=Count(100) 
  a=a[Count(1,10)//Count(21,30)]  # retain ranges 1:10 and 21 to 30 

 
 delete t.A>1 
 delete t[{1 3 5}] 

delete alias

delete alias
see alias delete alias_name . Example:

 
alias ls list 
alias delete ls 

Delete from database

delete molcart table s_dbtable [connection_options]

Deletes table from Molcart database with all index tables, related indexes and metadata. Database connection may be specified by connection_options

Delete plots from the table

delete plot table [name=s_handle]

This command deletes from the table all plots or only the plots with the specified name (see make plot).

ICM table plots are stored in the table header as an sarray T.plot, so 'delete plot T' is identical to 'delete T.plot'

delete selection variable

delete as_selectionName
or
delete vs_selectionName
delete named variable with atom or v_ selections. The number of named selections is limited to about 10 in each category, therefore you may need to delete them from time to time.
Important: keep in mind that deleting the named selection is not the same as deleting actual objects, molecules or atoms selected by them. To delete atoms selected by a named variable in an non-ICM object, add keyword atom (see delete atom nameSelection )
Examples:

 
 build string "ASFGD"      # build a molecule  
 vsel = v_//phi,psi    # this is a vselection  
 delete vsel 
 
 asel = a_//c*,n*      # this an aselection (atom selection)  
 delete asel           # delete variable asel, do not touch the atoms 
 delete atom asel      # delete atoms in a non-ICM object 

delete variable array {i_elementNumber|I_elementNumbers}

delete one or more elements from any array. If the array is a column in a table T, use the delete T[i] command which can delete both a single row, e.g. delete t[2], or a row selection.

Examples:

a={1 2 3}
b={1. 2. 3.}
c={"a" "b" "c"}
delete variable a 2  # deletes the 2nd element of the array
show a
 {1 3}
delete variable b 2
delete variable c 2
#
a = Count(100)
delete variable a Count(50)*2 # deletes even numbers

delete variable pairdistArray I_pos

Removes elements at positions I_pos from the array

delete atom

delete as_atoms

delete atoms as_namedSelection
delete selected atoms in a non-ICM object. The selection here must be a constant atom selection, rather than a named selection (e.g. you can say delete a_/1:10/* but NOT aaa = a_/1:10/* , delete aaa ).
To delete a named variable, use delete atom name Example:

 
  read pdb "1crn" 
  delete a_/1:10/*   
 
  aaa = a_/18:20 
  delete atom aaa 

 
delete directory "/home/doe/temp/" 

delete system s_fileName s_fileName ...

delete external file.

Example:

delete system "/tmp/aaa"

See also other internal icm equivalents of the system commands that allow to avoid new threads.

command	comment	unix equivalent
copy-systems_f1 s_f2	copy a single file	cp file1 file2
rename system s_f1 s_newname	rename/move a single file	mv file1 file2
make directory s_dirname	make a directory	mkdir
set directory s_dirname	change directory (cd)	cd dirname
delete directory s_dirname	delete an empty a directory	rmdir
Path ( directory )	returns the path to the current directory	pwd
Sarray ( s_filename_filter directory [ all ] )	returns the file list array, all goes to subdirectories	ls -1 [-R] namepattern

delete history lines

delete session
deletes all previous history lines. Example:

 
call _macro 
delete session 

delete hydrogen chem [all]
delete selected hydrogen atoms in a non-ICM object or a chemical array. See also build hydrogen. To delete hydrogens in an ICM object, strip it first.

When the hydrogens are deleted in a chemical array, the default is to preserve the chiral hydrogens in fused rings (the regular chiral hydrogens will still be deleted). To delete all hydrogens use option all . In the latter case when the hydrogen carrying the stereo bond is deleted for all heavy atoms including fused rings and the stereo bond will be reassigned to one of the heavy atom neighbors.

Example:

build string "ASD"
strip # makes a non-ICM object
delete hydrogen a_/2,3/h*
#
group table t Chemical("[C@@](C)(N)[H])O") "mol"
delete hydrogen t.mol all # all hydrogens gone

 
   delete object          # delete ALL molecular objects 
   delete a_*.            # delete ALL molecular objects  
   delete a_2,4.          # delete objects number 2 and 4  
   delete a_2a*.          # delete objects with names starting from 2a  
 
   read pdb "1crn"        # load crambin  
   convert                # create the second object named 1crn_icm  
                          # from the pdb object  
   delete a_1.            # delete the 1st pdb-object  
   delete Object( as_graph )  # graphical selection  

 
   read pdb "2ins"        # load insulin with water molecules  
   delete a_2ins.w*       # delete water molecules  
   delete atoms as_graph  # deletes selected non-ICM atoms/molecules 
   delete Mol( as_graph )  # deletes selected non-ICM atoms/molecules 

 
   read pdb "newmol"              # automatic bond determination is not perfect  
   delete bond a_/3/cg1 a_/5/ce2  # disconnect two carbon atoms  

delete column T [inverse] [ I_cols | S_cols | selection | iarray | rarray | sarray | parray | i_from [ito] ]

delete columns in a table T. Option inverse keeps the specified columns and delete the rest. You can select columns in multiple ways:

• by array of indexes : e.g. 3//4//5
• by array of column names :
• by GUI selection:
• by column type: e.g. rarray sarray
• by column index range: e.g. 3 (meaning all except column 1 and 2)

Example:

   add column t 1//1 2//2 3//3 'a'//'b' 5.5//5.5 6.6//6.6 's'//'s'
   delete column t 3  # starting from column 3
   delete column t 3 5 inverse  # all except 3,4,5
   delete column t iarray rarray 
   delete column t 't.A'//'t.B' inverse # delete all except columns 'A' and 'B'

See also: rename column tab ..

delete conf

delete conf i_stackConfNumber [os_obj]

delete conf i_confNumberFrom i_confNumberTo [os_obj]

delete conf I_stackConfNumbers [os_obj]
delete a specified conformation from the stack or a series of conformations starting from i_stackConfNumber to i_stackConfNumberTo . An integer array of indices can also be provided.

if the os_obj argument is provided the changes above will be applied to the local stack in the object.

See also:

• load conf
• store conf

 
   delete drestraint a_mol1 a_mol2       # intermolecular restraints  

 
   delete label # deletes all labels
   delete label 1  # delete the first displayed label  

delete label chemarray [all] [index=I_]

deletes atom annotation in 2D chemical spreadsheet. Without the all option the command will only remove labels from the selected atoms, otherwise all labels will be removed. The selection can be done in the GUI and it appears as a green halo around select atoms.

Example:

# create annotated chem table
add column t Chemical({"CCCCN","CCCNCCC","CC(=O)O","C(=O)O"}) 
add column t Predict( t.mol "MolpKaBase" ) name="pkab"
add column t Predict( t.mol "MolpKaAcid" ) name="pkaa"
set label t.mol t.pkab window = {0.,14.}
set label t.mol t.pkaa window = {0.,14.}
# now delete it
delete label t.mol all

See also: set label chemical

delete link

delete link ms

delete links to sequences and alignments for selected molecules

delete link variable

delete all groups of linked variables (e.g. unlink the variables), see also link variables .

delete map

*delete { *map | s_mapName } delete s_mapName or all maps.

delete sequence i_minLen i_maxLen

(to delete a sequence form alignment use the only option, see below).

• selection : delete the sequences selected through GUI.
• compress : delete the sequences not included in the alignments, i.e. freely floating sequence not included in any alignments, (compare with the compress option of delete )
• protein or peptide will delete only amino-acid sequences,
• nucleotide will delete only DNA or RNA sequences,
• unknown : delete sequences with more than 20% of 'X' or 'x' residues. Note that this option changed its meaning. Previously it was same as compress.
• by sequence length, (e.g. delete sequence 1 50 )

• no arguments: delete all ICM-sequences
• one integer argument: delete last n sequences from the sequence list
• two integer argument: delete sequences shorter than i_minLength or longer i_maxLength

delete alignment only selection

delete alignment only seq1 seq2 ...

To delete sequences selected via the graphics user interface from an alignment without deleting them from the shell. Example

 
  delete sh3 only Fyn 
  delete sh3 only selection 

delete site ms1 [{s_Site|i_number|I_numbers|pattern=s}]

delete site rs
delete the sites of the selected molecules. The sites can be specified by their name, or number, or residue selection. All sites are deleted by default.
Example:

 
   nice "1as6"          # has 3 sites, one in each molecule.  
   delete site a_1.1 {1} 
   delete sites         # delete all of them 

delete site ali [i_number] [I_box]

deletes annotation in the alignment by i_number or inside the I_box.

See also: set site alignment

 
           # SS-bond specified by residue, or  
   delete disulfide bond a_/15 a_/29         
           # by atoms 
   delete disulfide bond a_/15/sg a_/29/sg   
           # remove all SS-bonds in the current object 
   delete disulfide bond all                 

 
   delete peptide bond a_/15/c a_/29/n  

delete conformational stack inside an object

delete stack os

deletes the compressed stack inside the specified object.

See also:

• store stack object
• load stack object
• montecarlo .. store
• set object .. stack
• Exist ( os1 stack )

delete parray elements

delete parray[i_index]

delete parray[I_index_list]

deletes specified elements from a parray.

Example:

C = Chemical({"C","CC","CCC","CCCC","CCCCC"})
delete C[{1,3,5}]
delete C[1]

 
   group table t {1 2 3} "a" {4. 5. 7.} "b"   
   delete t.a == 2       # the second entry  
   show t 
   delete t[2]           # the second entry  
   show t 
   delete t              # the whole thing  
   group table t {1 2 3} "a" {4. 5. 7.} "b"   
   delete t.a > 1          # 2nd and 3rd

 
   delete terms "tz,sf"    # do not consider tethers and solvation contributions  

delete selftether [ as]

deletes internal tethers for selected (or all atoms)

See also:

• selftether
• set selftether
• term ts
• convert
• set tether

delete tether

delete tether [ as]

delete tethers of the specified atoms ( as_ ), if no selection is specified all tethers in the current object are deleted.

delete tether loop [ as] - this tool deletes tethers for residues flanking insertions and deletions (one residue on each side), as well as N- and C- termini. The tool is used to help the minimize tether command to build a more relaxed loop or end.

delete a tree from a table header array

delete variable treeParray i_treeIndex

deletes a tree object (generically considered as a parray )

Example:

make tree T  
delete variable T.cluster 1

delete chemical chemarray

deletes selected parts of the chemicals. See select chemical command.

display

[ display model | Display new | Display offscreen | display origin | Display rotate | display stack | display box | display clash | display drestraint | display gradient | display grob | Display grob label | display hbond | Hbond color | display label | display map | Display trajectory | display ribbon | display site | Display skin | display slide | display string | display tethers | display volume | display window | Display gui ]

display [transparent] [stick|skin|ribbon [base]] [as [as_2]]
display specified graphics primitives for selected atoms or residues.

Once something is displayed and your cursor is in the graphics window you may rotate, translate, zoom and move both clipping planes with the mouse and keystrokes.
To refer to the base part of DNA/RNA represented as ribbon , use the additional specifier called base, which can be separately displayed and colored. E.g.

 
 makeDnaRna "ACTG" "mydna" yes yes "dna" 
 display ribbon  
 color ribbon base a_1 blue 

 
read pdb "1crn" 
display transparent ribbon 
display skin transparent 

 
 build string "AFSGDH;QWRTEY"       # two peptides 
 display                        # display current object and color atoms   
                                # according to atom type  
 display a_1 red                # display the first molecule and color it red  
 display skin a_/5 a_* yellow   # display skin of the 5th residue  
                                # as surrounded by all the atoms  
 display ribbon                 # display ribbon for all the residues  
 
 read pdb "2drp"                # a pdb file 
 assign sstructure a_a/123:134,153:165 "H"       # No sstructure in 2drp  
 assign sstructure a_a/109:114,117:121,141:144,147:151 "E" 
 display a_a ribbon red                          # two Zn-fingers  
 display a_a/113,116,143,146/!n,c,o xstick blue  # Cys residues  
 display a_a/129,134,159,164/!n,c,o xstick navy  # His residues  
 display a_m,m2 cpk magenta                       # Zn-atoms   
 adna1=a_b//p,c3['],c4['],c5['],o3['],o5[']      # two DNA chains   
 adna2=a_c//p,c3['],c4['],c5['],o3['],o5['] 
 display adna1 xstick white 
 display adna2 xstick aquamarine 
 display adna1 adna1 surface white 
 display adna2 adna2 surface aquamarine 
 center 
 display "Zn-finger peptides complexed with DNA" pink 
 
# display 4 chains of insulin as 4 thick worms colored from N-to C-terminus 
 read pdb "2ins" 
 color background blue 
 assign sstructure a_/* "_"  # thick worm representation 
 GRAPHICS.wormRadius= 0.9 
 display a_/* ribbon only 
 color a_1/* Count(1 Nof(a_1/* )) ribbon 
 color a_2/* Count(1 Nof(a_2/* )) ribbon 
 color a_3/* Count(1 Nof(a_3/* )) ribbon 
 color a_4/* Count(1 Nof(a_4/* )) ribbon 
 
# examples of DNA and RNA ribbons 
 nice "4tna" 
 resLabelStyle = "A" 
 display residue label 
 color residue label a_/?u gold # ??u also selects modified Us 
 color residue label a_/?a red 

display new

display restore

display restore plane

commands to mimic some of the interactive controls. These commands are primarily used in GUI commands ( see icm.gui file) and scripts/macros.
new : rebuilds some graphical representations (e.g. your as_graph has been changed in the shell and you need to refresh the image, or you changed the orientation and want to redisplay the labels elevated above the skin surface by resLabelShift ).
restore : a softer action than new .
restore plane : moves the clipping planes beyond the displayed objects (keystroke: Ctrl-U, or the 'Unclip' button) .

 
   display off 400 300 
   nice "1est" 
   rotate view Rot( {0. 1. 1.} 50.) 
   write image "est1" 
   unix xv est1.tif 
   set window 700 800  # NB: 'center all' will be applied 
   write image "est2" 
   unix xv est2.tif 
   display a_/4/o cpk 
   center a_/3,4 
   write image "est3" rgb 
   unix xv est3.rgb 
   build string "se ala trp" 
   display off 400 300 
   display skin 
   write image "est3" rgb delete 
   unix xv est3.rgb 

 
 read pdb "1crn" 
 display 
 display origin 
 undisplay origin 

Setting rotation or rocking mode

display rotate [on|off] [ i_NofCycles ] [pause]

The graphics view can be set so that molecule is continuously rotating or rocking, but the ICM session remains interactive. This mode can be set with the above command. The style of continuous interruptable movement is controlled with the GRAPHICS.rocking preference. Specifying the number of rotation or rocking cycles i_NofCycles is useful for movie making. The pause option forces the command to finish the requested number of rotations before proceeding to the next commands, as opposed to just launching the rotation and proceeding with the rest of the script.

Example:

GRAPHICS.rocking = "xY-rocking"
display rotate on 3 # three cycles

See also: write movie , GRAPHICS.rocking

display stack

display stack [ os_withStoredStack ] [iFrom iTo] [loop [=nCycles]] [r_NofInterpolationFrames [simple|cartesian]] [center] [reverse] [sstructure] [auto]

interpolated display of conformational stack of its parts. Aruments and options:

• optional os_withStoredStack . If this argument is missing, the global stack will be used. With the argument the built-in local object stack will be played out.
• optional start and end frames: iFrom iTo
• option loop [ = nCycles ] : the command makes a video loop and repeats it 99999 times. Optional nCycles redefines the number of repetitions.
• r_NofInterpolationFrames [ simple | cartesian ] ] (e.g. 10.0 cartesian ) : determines the number of intermediate frames. The following interpolations are currently provided:
  • simple : just wait for the specified number of frames
  • cartesian : perform linear interpolation between stack conformations
  The default interpolation is simple .
• option center : centers on the displayed atoms
• option sstructure : recomputes secondary structure for each stack conformation.
• option auto : extracts the number of cycles (1 or endless loop) and the number of interpolated frames ( no interpolation or a fixed number of interpolated frames) from the stack itself. The two parameters can be set with the set stack os loop|fast [off] command. The GUI interface for the object stack display uses the auto option.
• option reverse : toggles iteration between first and last frame back and forth. (Doesn't jump from the last frame to first, instead goes reverse to the first)

Example:

  build string "ASDFW"
  montecarlo v_//x* mncalls=10 vwMethod=2 # create a conformational stack
  display xstick cpk  only
# the previous commands just prepare stack and display
  display stack 20. cartesian loop=4 center # repeat 4 times and stop

# make the same preparations
  write movie "peptamovie" on exact
  display stack 20. cartesian loop=1 center # repeat 4 times and stop
  write movie exit

The display stack command is somewhat similar to the display trajectory command. The display stack command has the following benefits:

• it recomputes the skin if the skin is present
• does not mess up the C-terminus in case of local deformations
• does not save or use any external files.
• it allows easy looping with the loop [= nCycles ] option.

See also:

• display trajectory
• write movie
• store frame
• stack

display box

display box [ R_6boxCorners ]
display graphics box specified by x,y,z coordinates of two opposite corners of a parallelepiped. This box can be resized and translated interactively with the Left and Middle mouse buttons:

• Resizing: Grab a corner of the box with the Left-Mouse-Button and drag it to resize the box
• Translating: Grab a corner or a center of the box with the Middle-Mouse-Button and translate

See also the Box () function which returns six parameters describing the box.
Examples:

 
   build string "se ala his gly met" # a peptide  
   display 
   display box                      # the default box   
   display box {0. 0. 0. 2. 2. 2.}  # define position/size 
   display box Box(a_/2 )           # surround the a_/2 by a box  
   display box Box(a_/2 1.2)        # or add 1.2A margin 

display clash

display clash [ as_1 ] [ r_clashThreshold ]
display all the interatomic distances for selected atoms which are shorter than the sum of van der Waals radii multiplied by the r_clashThreshold parameter. The default value is taken from the clashThreshold variable. Initially it is set to 0.82 but can be redefined. IMPORTANT: this will work only for the ICM-objects. For hydrogen bonded atoms the threshold is additionally multiplied by 0.8. Use the show energy "vw" command (and pay attention to the current fixation) to precalculate interaction lists.
This command may show some irrelevant short contacts. calcEnergyStrain , display gradient , etc. seem to be more informative.
See also: GRAPHICS.clashWidth , clashThreshold , show clash, undisplay and atom energy gradient (force) analysis with: show a_//G or display a_//G.
Example:

 
 read object s_icmhome+"crn" 
 show energy "vw" 
 display a_
 display clash                  # all clashes, default clashThreshold=0.82
 undisplay clash 
 display clash a_/11 0.95  	# distances < (R1+R2)*0.95  
# this is an alternative method which analyzes the gradient 
 selectMinGrad = 100.   	# analyzes forces greater than 100 
 display ribbon grey 
 display Res( a_//G )  
 display gradient a_//G 
 color Res( a_//G ) ribbon magenta    

 
  build string "se ala his trp ala gly gly" 
  display 
  set drestraint a_/1/hn a_def.a1/6/o 2  
  show energy "cn"
  display drestraint 
  minimize "vw,14,to,cn" 

 
 build string "ala his trp glu leu" 
 randomize v_//phi,psi 
 show energy 
 selectMinGrad= 20.
 display a_ 
 display gradient a_//G 

• dot will show only dot-vertices of the object.
• reverse to invert lighting; this option will change directions of the grob surface normals (will turn the grob inside-out)
• smooth enforces the Gouraud shading method to smooth the solid surface.
• solid allows solid surface representation of the object and requires that the original object has information about triangles forming the solid surface.
• transparent makes solid grob transparent

 
   read matrix s_icmhome+"def.mat"    	# 2D sin(r^2)/r^2 function of a grid 
   make grob solid def      		# convert matrix into a graphics object g_def 
   display g_def smooth     		# a hat of the 22st century  
   rotate view Rot({1. 0. 0.}, 45.)     #  
   display g_def reverse    		# shine light from inside the head 
   display grob smooth transparent 	# like Lenin in Mausoleum  

set font of a 3D label

display g_label [bold ] [ italic ] [ underline ] i_Size [font=s_FontName] [rgb=R_3rgb|"#xxyyzz"]

displays g_label text (technically it is a grob with a single point and associated text) in a particular font.

Example:

read pdb "1crn"
display a_
label3d = Grob("label",Mean(Xyz(a_/3,4)), "3D label for res 3,4")
set font label3d times 36 rgb="#00ffdd"
display label3d
select edit label3d # makes it movable, press Esc to get rid of the cursor

The color or hydrogen bonds will be calculated according to a calculation involving the effective lone pair density (see hbond color ).

See also: undisplay hbonds, show hbonds.

Strength and color of a hydrogen bond

The hydrogen bonds created or displayed with the make hbond or display hbond commands are colored according to the estimated 'strength' of this hydrogen bond. This is just an estimate since the energy of hydrogen bond is not easily decoupled from the van der Waals and electrostatic contributions between the hbonded atoms and their immediate environment. In ICM the strength is estimated using the following procedure described in J Med Chem. 2003 Jul 3;46(14):3045-59.

For a hydrogen bond acceptor atom A(i) and a hydrogen atom H(j) located at r_j, the hydrogen bonding interaction was estimated

F_{ang(phi)Fdist} (r_LPi -r_j)

, where phi is an angle formed by the hydrogen bond acceptor atom, hydrogen, and the hydrogen bond donor, and r_LPi is the radius vector of the center of the lone electron pair (LP) closest to the hydrogen. The angular function used was defined as F_ang = 1 - cos(k*phi) . Parameter k is accessible as GRAPHICS.hbondAngleSharpness in the shell. Distance function F_dist (r_LPi-rj) was constant (1.0) within L_HB/2 from the lone pair center and dropped as

exp( -(((r_LPi - r_j)/LHB) - 0.5)² ) .

beyond that distance, where L_HB is the characteristic range of hydrogen bonding interaction (value of L=1.6 �was used). Lone pair centers were placed at 1 �from the hydrogen bond acceptor atom, assuming symmetrical planar trigonal configuration for sp2 atoms and tetrahedral configuration for sp3 atoms. The resulting functional dependence reflects (at least qualitatively) the physical nature and observed statistics of the hydrogen bond interactions. The interaction is maximized when the hydrogen atom is pointing directly to the acceptor atom along a lone pair axis and drops quickly as the hydrogen is moved farther away. The strength declines more gradually as the hydrogen moves out of the LP axis or, as hydrogen bond donor, hydrogen atom, or hydrogen bond acceptor, move out of alignment.

See also: GRAPHICS.hbondMinStrength

display label

display [{ atom | residue }] label [selection]
display variable label v_selection
a graphics label with atom name, residue name, variable name for all or selected atoms, residues or variables respectively. The text of this label is not user-defined, although you can control it in two different ways. First, residue label style can be set using either Ctrl-L in the graphics window or resLabelStyle preference , and variable label style either by Ctrl-V, or setting varLabelStyle preference. Second, the ICM-shell string variable s_labelHeader defines a prefix string for all labels. For example, if you display CPK atoms you may move the label to the right from the atom center by s_labelHeader=" " .
The _aliases file has convenient aliases (e.g. ds for display, unds for undisplay, re , for residue, va for variable) for those of us who like typing commands. In this case you may just type ds va la to display variable labels, etc.
Examples:

 
 build string "FAHSGDH" 
 display a_
 display residue label #  
 undisplay label 
 display residue label a_/his 
 display variable label v_//phi,psi 
 display variable label v_//* & as_graph 
 display atom label a_/1:3/* 
 undisplay label 
# or with aliases: 
 ds re la a_/1,3 
 unds la 
 .. etc. 

• 0 - transparent/invisible
• 1 - blue
• maxNumer - red

 
   build string "se his arg"  
   make map potential "el"  Box( a_/1,2/* , 3. )  
   display a_ 
   display map m_el {1 2 0 0 0 0 3 4 5 6} {-20.,100.}
   center
   make grob m_el 2. name="g_1"
   make grob -m_el 1. name= "g_2"  
   display g_1 red 
   display g_2 blue 

Arguments and options:

• Integers i_From and i_To specify the frame range.
• Real values r_Smooth1 and r_Smooth2 determine minimum and maximum smoothing parameters (i.e. number of additional frames, inserted if conformation change is too dramatic). For example: 100. 700.
• Specifying atom selection as_1 defines a certain fragment on to the initial conformation, of which subsequent conformations are superimposed.
• The image saving options include: image [ =s_framePath ] [ rgb|targa|png|gif ] Option image allows one to automatically save a series of image files in the s_framePath argument of the image= option or in the default s_tempDir directory.
• center option with selection as_2 determines a fragment for graphics window centering (all, if center without as_2 ).

To obtain the trajectory info use
read trajectory s_TrjFileName
When playing a trajectory, you can use ICM interrupt ( Ctrl-\ ) to stop, and then toggle stepwise frame playing, reverse, or quit playing. The default is to play a whole trajectory without smoothing, superimposition or centering. Example:

 build string "ala ser ala thr ala glu ala"
 mncallsMC=10000                         # 
 montecarlo trajectory
 read trajectory "def"
 ds ribbon, wire
 ds trajectory center sstructure  10.

• do not forget to start ICM with the -24 flag to double the image quality.
• set IMAGE.generateAlpha to no if you want to keep the background colored and not transparent.

Allowed image formats are: rgb, targa, png, gif . The file extensions will correspond to the image file format. The image file names consist of the default path and name, appended with the frame number. Example:

 
 display trajectory image="/tmp/f"  
 /tmp/f_1.png 
 /tmp/f_2.png 
 ... 
 s_tempDir = "/home/jack/X" 
 display trajectory image rgb 
 /home/jack/X_1.rgb 
 /home/jack/X_2.rgb 
 ... 

display ribbon rs color

displays protein or DNA backbones in ribbon presentation.

See also:

• ribbon
• undisplay
• ribbonStyle
• GRAPHICS.ribbonCylinderRadius

display { skin | surface } as_1 as_2

display skin as_1 molecule
display analytical molecular surface, also referred to as skin, or solvent accessible surface area . Each display skin command will delete the previously displayed skin in the current plane. To display several different skins, use the set plane command to change the current graphics plane before you issue the display skin command. You can also convert the skin into a grob with the make grob skin command. You can co-display many grobs on the same plane, as well as make the grob transparent. This grob can be further split into individual shells with the split command.

Options:

• molecule : (for skin) considers each molecule in isolation

See also: How to display and characterize protein cavities.
Example:

 
   build string "se ala his glu"  # test tripeptide  
   display                        # the wire model  
   display skin a_/1 a_/1         # skin around the 1st residue or just press <F1> 
   display skin a_1 molecule      # equivalent to a_1 a_1
   set plane move on 2            # key with your cursor in the graphics window 
   display skin a_/3 a_/3         # skin around the 3st residue 
                                  # now you can toggle planes with F2 and F1 
   display surface                # solvent-accessible surface 

display slide [ reverse | i_slide ] [s_slideProperties] [ view ] [ smooth ] [ add ] ]

display the next slide or slide number i_slide . Options:

• which slide to show? if you have just said: display slide the next slide will be shown, display slide reverse will show the previous one. A specific slide number i_slide can also be shown ( ICM also understands index=3 ).
• view : using only the viewpoint/clipping planes from a slide (see also set view ).
• smooth : or smooth= i_transition_time_in_msec will make a smooth view transition from the current state to the slide view. (e.g. display slide smooth or display slide 5 smooth=1000
• add : adding representations to the existing display, rather than overwriting the slide (like appending a new graphical layer)

You can individuall control which sections of the slide information to use in display slide using s_slideProperties . The syntax of this string is the following: "sect1on;sect2on;..;-sect3off;sect4off; .." The section names are separated by a semicolon, and plus and minus are used to switch things on and off with respect to the default state. The allowed sections include:

Section Name	Default	Description
"layout"	-	if +, sets the layout of ICM windows and panels (if off, preserves the current layout)
"activewindows"	+	if +, sets the saved active window or panel in ICM gui
"smooth"	-	if +, makes smooth animated view transitions between slides
"add"	-	if +, adds the next slide as a layer to the previous, rather than overwrites it
"gf"	+	graphical representations (CPK, xstick, skin etc.)
"color"	+	colors of representations
"labeloffs"	+	restoring slide-specific displacements of residue labels
"viewpoint"	+	the view point, zoom, and clipping planes
"graphopt"	+	the state and parameters of rotation, rocking, etc.
"mol"	+	if - , do not restore any property of molecular objects in main graphics window
"grob"	+	if - , do not restore any property of grobs in main graphics window
"map"	+	if - , do not restore any property of maps in main graphics window
"all"	-	switches all sections, on (+) or off (-)

Examples:

 display slide 4 "-all;+gf;+color"
 display slide 4 "-viewpoint"
 display slide 4 "+smooth" # enforce smooth view transitions

display slide show [ index=i_start ] [reverse]

the keyword show switches the program into the slideshow mode and makes smooth transition the default. Other options are the same as above.

Examples :

icm -g&
read binary s_icmhome+"example_slideSGC.icb"
display slide
display slide # the next slide
display slide smooth # make a 500msec-transition 
display slide 4 # 5th slide 
display slide 2 view  # enforce viewpoint from slide 7
display slide add 2 # display additional representations from slide 3

See also: add slide , set view .

display string

display string s_StringText [P_image] [size=r_imageScale] [color_spec] [font_spec] [ r_XscreenPosition r_YscreenPosition ]

display a text string in the graphics window. Relative X and Y screen coordinates (ranging from -1. to 1.) of the string beginning may be specified to display the string in a given location. Defaults are x = -0.9, y = 0.9, i.e. upper left corner of the screen.

The string can be dragged later to any location by the middle mouse button.

The command supports various formats for specifying the label color color_spec and font parameters to characterize the label font font_spec.

Two fonts are at your disposal: the default font (usually times) and the auxiliary font (usually symbol). Both fonts can be redefined by the set font command. You can also switch to the auxiliary font and back inside the string by backslash-A ( \A). (.e.g "Red: \Aa\A-helix"). You can also list and delete your string labels by the list label and delete label commands.
Examples:

 
display string "Crambin"                            # a simple string  
 
display string "Act.site of \Ab\A-lactamase" yellow # Greek beta letter  
 
build string "ala" 
display string Name(a_1.) red 28, 0. 0.9     # first object name  
                                             # in the middle  
                                             # (font size=28)  

display volume

activates fog from the command line. See also fogStart . Accordingly, the undisplay volume switches the effect off.

display window

display window [ i_xLeft i_yDown i_xSize i_ySize ]

undisplay window

displays/undisplays the graphics window. When ICM is started without GUI, it is allowed to specify the window size and position.

See also: set window

display window=s_windowList

undisplay window=s_windowList

Displays/undisplays GUI windows and toolbars. s_windowList should be a comma-separated list with ICM panel and toolbar names.

• "opengl" # undisplays the graphics window
• "all" # undisplays all except graphics window
• "alignments"
• "htmls"
• "masterview" # shows/hides workspace panel
• "moledit" # shows/hides molecular editor window
• "plotdialog" # shows plot dialog for the current table (in modal mode)
• "searchwindow" # show/hides chemical search space window. Chemical pattern can be provided optionally as an extra argument
• "columnfilter" # launches column filter dialog for specified table column
• "tablesearch" # launches table "Find and Replace" for the active table. Search string can be provided optionally as an extra argument
• "processes" # shows/hides background job list window
• "prop" # 'Display Panel' with multiple tabs (display/light,...)
• "terminal"
• "tables"

• "moveTools"
• "clipTools"
• "miscTools"
• "viewTools"
• "planeTools"
• "fileTools"
• "selecionTools"
• "tableTools"

You can also display/undisplay individual tabs from the 'Display Panel'. To do that you need to append a tab name to the "prop:".

Example:

undisplay window="prop:light"   # hide 'light' tab from the panel

Note: This command does not affect the content of the main working area (the center)

Example:

read binary s_icmhome + "example_search.icb"
display a_
undisplay window="tables" # hides tables 
undisplay window="all"    # leaves only 3D graphics window
display window="moledit" Chemical("CCO")  # popups Molecular Editor with compound
display window="searchwindow" Chemical("CC[O;D1]")  # popups Chemical Search Space with compound

display window=s_window center

sets the specified s_window to the center. Windows which may occupy the central position are:

• "opengl"
• "alignments"
• "htmls"
• "tables"

Example:

read binary s_icmhome + "example_search.icb"
display a_
display window="opengl" center # sets graphics window to the center

display window=s_layoutString

Applies the window layout specified in the s_layoutString. ICM stores the layout information as a string in a specific format. Window layout information is stored, for example, in slides.

Example:

read binary s_icmhome + "example_search.icb"
sl = Slide()
display a_
display window=String(sl gui) #changes the view back to what was before the 'display' command

See also: Slide, String slide gui

display GUI windows

display gui [off] s_window

Obsolete command. See: display window

 
   edit mncalls   # actually it is easier to type: mncalls=333 
   edit FILTER    # edit a system table, do not change names of components 
# 
  group table t {1,2,3} "A" {"a","b","c"} "B"  	# create a table
  t						#
  edit t					# edit table t 

 
   macro threeEssentialsOfLife          # declare new macro  
                                        # define essentials  
      l_info=no 
      modes={"\n\tOoops!!\n","\n\tOuch!!\n","\n\tWow!!\n"} 
                                        # randomly pick a line  
      print modes[Random(1,3)] 
   endmacro 
   threeEssentialsOfLife                # invoke macro  

enumerate charge {chemarray|chemtable} [r_pH=7] [window=r_window(2.)] [name=s_result]

Generates all possible formal charge states at given pH level and window

Enumeration of stereoisomers

enumerate chiral chem_array [index=I_selectedChems] [center=i_Max_Number_of_Centers] [name=s]

Generates all possible stereo isomers for each chemical compound from or from selected chemicals ( I_selectedChems ). Important: this operation requires that two conditions are satisfied:

• a molecule has a stereo center (i.e. an sp3 atom with four different substituents
• if a stereo center has a definite chirality ( "up" or "down", or R, or S) stereo isomers will not be generated. The center needs a stereo bond is marked by type "off", or "either" to imply an uncertain chirality or a racemic mixture of two isomers.

Sometimes you may want to skip compounds with number of unspecified centers greater than certain value. In this case you should provide center = i_Max_Number_of_Centers argument to the command.

The command will always generate at least one element for each compound. Example:

group table t {"CC(N)O","CC(C)C(C)O"} "mol"
enumerate chiral t.mol name="isomers" # creates isomers.mol

Tautomer enumeration

enumerate tautomer chem_array [keep] [filter] [index=I_index_array] [name='T_tauto']
Generates all possible tautomers for each chemical compound from . Returns the resulting chemical array of tautomers. The command will always generate at least one element for each compound.

The current function only generates tautomers that preserve the atom content (does not add or remove hydrogens). With keep option it'll also preserve the hybridization state of each atom (i.e. does not change sp3 to sp2).

Some tautomers are formally possible but chemically do not make much sense. To avoid generating those tautomers, Split uses the TAUTOFILTER.tab file that contains the unwanted or chemically impossible tautomer patterns in the SMARTS format. Feel free to add more patterns to this file. Use filter option to enable filtering by patterns.

Example file:

#>T TAUTOFILTER
#>-sm----------------comment
"*C([OH1])=[N;R0]"  "peptide bond"

 
 p = Chemical( "C(=C(NC(=N1)N)N2)(C1=O)N=C2" )
 Nof(p) # 1 element 
 1 
 enumerate tautomer p
 show T_tauto
#>T T_tauto
#>-mol---------idx--------
  "C1=NC2=C(NC(=N)NC2=N1)O" 0
  "c1nc2=C(NC(=N)N=c2[nH]1)O" 0
  "C1=NC2=C(N=C(N)NC2=N1)O" 0
  "c1nc2c(nc(N)nc2[nH]1)O" 0
  "C1=NC2=C(NC(N)=NC2=N1)O" 0
  "c1nc2C(NC(=N)Nc2[nH]1)=O" 0
  "c1nc2C(N=C(N)Nc2[nH]1)=O" 0
  "c1nc2C(NC(N)=Nc2[nH]1)=O" 0
  "c1nc2C(=NC(=N)Nc2[nH]1)O" 0

Combinatorial library enumeration

enumerate library [simple] chem_scaffold_R1R2 .. chem_R1 chem_R2 .. \ [name= s_libTableName|output= s_fileName] [filter=expression]

Applies chemical arrays (usually a column in a chemical table) for each of replacement groups chem_R1, chem_R2 etc. to the first element of the scaffold template array. (also known as enumerate library

The scaffold.The scaffold structure needs to be drawn as a Markush structure, e.g.

add column scaffld Parray( "[R2]C(C(=O)[R3])NC(=O)N[R1]" ) name="mol"

The replacement groups.Each replacement group in a chemical array (table) needs to have an attachment point specified. In the Smiles/Smart representation used in ICM it is marked by an asterisk (e.g. "[C*]CC" ). Marking an atom as an attachment point can also be done in the Chemical Editor ( right-click on an atom and choose the Attachment Point menu item).

The output table or file.The output table will contain all combinations . If the output option is specified the resulting library is saved to a file and the table is not created. Warning: if the number of combination exceeds 20000 the resulting library is saved to a file automatically (to avoid memory problems).

• Option name = s_table allows one to change the default name of the output table.
• Option output = s_file forces the file output and suppressed the table creation.

The output chemical table has a product column as well as the index of each R-group.

simple option toggle a special mode where instead of full enumeration it simply goes through the input substituents and take i-th element from each. This mode requires that size of all R-group arrays should be the same. The size of the output will be equal to the size of R-group array(s)

Dynamic filtering of the output by applying a filter expression.The filter= s_expression option allows one to apply a filter during the library generation. The filter expression is a double-quoted string with the following structure: "Function1 relation value & or | Function2 relation value & or | .. "

Example:

filter = "MolLogP(mol)<5. & Nof_Frags('C(O)=O')<1"

<> See also:

• Predict for a detailed description of some of the functions.
• make reaction

A short form of the enumerate library command and linking. The replacement group arrays can be linked to the R positions of a scaffold with the link group command. In this case a short form of the command can be used, e.g.

link group scaffold.mol 1 r1.mol 2 r2.mol 3 r3.mol
enumerate library scaffold.mol

Example:

 read binary "example_enum.icb" # contains scaffold and R1,R2,R3
 enumerate library scaffold.mol[1] name=Name( "lib", unique ) R1.mol,R2.mol,R3.mol
 split group scaffold.mol[1] lib.mol   # if you want to split it back

The inverse operation: split the library into scaffold and replacement group arrays.A library can be also reduced back to the scaffold and replacement groups using the split group scaffold library command. E.g. split group scaffld.mol combilib.mol

See also: make reaction , split group , Replace chemical .

endwhile

endwhile
is one of the ICM flow control statements, used to perform a loop in ICM-shell calculations. See also while .

[ Find alignment | Find database | Find database fast | Find molecule | Find chemical | Find pdb | Find prosite | find pattern | Find molcart | Find table | Find pharmacophore ]

• find pdb: search a database of a single structure for a fragment with a given sequence pattern and partial structural similarity (e.g. loop ends match).
• superimpose: performs structural superposition, the command can do it on the basis of sequence alignment on the fly.

 
 read pdb "1nfp" 
 read pdb "1brl.b/" 
 rm !Mol(a_*./A ) 
 make sequences a_*. 
 aa=Align(1brl_1_b 1nfp_a) 
 ds a_1.//ca,c,n grey 
 ds a_2.//ca,c,n green 
 superimpose a_1.1 a_2.1 aa 
 center 
 find aa superimpose 
 show aa 
 
 gapExtension = 0.05 
 ab=Align(1brl_1_b 1nfp_a) 
 find ab 4. 0.7 superimpose 
 show ab                         # better 

See also: pairwise alignment multiple alignment

find database exact [ distance= i_nOfMutations]] options

find database pattern={ s_pattern | S_patterns } options

find database write [ s_database ]

find database fast [ = i_speed] [output=s_file] [name=s_tabName] # blast like fast search.
fast sequence or pattern search through a sequence database.
The default find database sequence search program performs a full gapped optimal sequence alignment, which is a global alignment with zero-end-gap penalties (ZEGA). These alignments are more rigorous (not heuristic) than popular BLAST of FASTA searches. The latest statistics of structural significance of sequence alignments derived for a number of residue substitution matrices will be applied ( Abagyan and Batalov, 1997 ) to assess the probability that a matching fragment shares the same 3D fold. The r_probabilityThreshold (default 0.00001 or 5.) option defines the lowest acceptable probability of hit. You can also provide a -logP number (e.g. 5.5 ) instead of a small probability ( 10^-5 ). Threshold of 10/DatabaseSize is usually a safe threshold (no guarantees though). Practically 10^-7 is a safe threshold for a SWISSPROT search (over 0.5M sequences). At 10^-4 you may find interesting hits, but a more serious analysis may be required to confirm its significance.
The second version of the command with the exact keyword performs a very fast search for identical or almost identical sequences. The distance= i_maxNofMutations parameter specifies the allowed number of mutations.
find database pattern

The third version of the command searches for string patterns in a sequence database. The sequence patterns can contain while cards (e.g. "A?[LIV]?\{3,5\}[!P]"). This search is very fast.
The fourth command find database write is used to export ALL sequences from the blast-formatted files into to an external FASTA file defined by output= string (default s_databasePath.seq ). This option is the inverse of the write index sequence command which creates several BLAST files from a FASTA file.
The common options are as follows: [ s_databasePath ("pdbseq") ] [ seq_1 .. ] [ ali_1 .. ] [ output= s_outputFileNameRoot ] [ name= s_tableName ] [ unique ] [ delete ] [ protein | nucleotide | type ]

• DATABASE: s_databasePath (default: "pdbseq" files in the $BLASTDB directory) defines the path of the three files with the compressed sequence files. For compatibility these three files (.bsq, .atb, .ahd) are the same as generated by the setdb (BLAST) command. The available files can be vied with the list database command, by default the "swiss" file is taken from the $BLASTDB directory. If the environment variable $BLASTDB is set, the three files will be taken from this directory. To read database files from any directory, specify its explicit path (e.g. "./myLocalDb" or "/home/user/myHomeDb1") Note: when the PDB sequences are updated, the blast files go into s_userDir + "/blastdb" , On Linux the database is at "~/.icm/blastdb/pdbseq" . To make this directory the default blast directory, reset the s_blastdbDir to "/your_home/.icm/blastdb/". In GUI, choose File;Preferences;Directories and modify the s_blastdbDir variable.
• QUERY: seq_1 .. (list of sequences), or ali_1 .. (list of alignments), or keyword selection determines which sequences will be searched against the database. The default (no argument) means that all the sequences currently present in the ICM-shell (see list sequence) will be searched. The selection can be made from the ICM GUI.
• OUTPUT FILES: option output= s_projName to redefine the name of the project. The default name of the output files is the name root of the database file. The following files are saved

   
   projName_seq  # query sequence(s) 
   projName.seq  # a sorted list of database sequences truncated to the matching fragment. 
   projName.tab  # the result table 
  

• TABLE: option name= s_resultTableName defines the names of output table which is created after the search. The table contains the boundaries of the hits, sequence identities etc.
• option margin= i_seqMargin in the pattern search defines the length of flanking sequences added to the matching fragment and saved in the s_projectName.seq file for further retrieval. Specify a very large number to store complete sequences.
• option delete will overwrite the output files without asking, as if l_confirm=no .
• option unique makes the program ignore hits with sequences 100% identical to the query set (if one sequence is a fragment of another, they are is still considered 100% identical).
• option protein or nucleotide limits the search to database sequences only of this type. It is important for PDB sequence database since it contains both protein and nucleic acid sequences.
• option type automatically selects protein or nucleotide based on the query sequence type, but only if you search with a single sequence.

• alignMinCoverage (default 0.5) a threshold for the ratio of the aligned residues to the shorter sequence length.
• alignOldStatWeight (default 1.) a parameter influencing the statistical evaluation of sequence comparison. To use run-time statistics use alignOldStatWeight=0.
• Up to mnSolutions hits will be retained in the final table of hits.
• The parallel version of the program will use the number of CPUs defined by the fork command (but not more than is available in your computer). The expected time is inversely proportional to the number of CPUs.
• maxMemory is a real ICM-shell-variable defining the size of the database buffer memory in Mb used by the command. If this size is smaller than the database, the sequences will be loaded in chunks.

 
#>T SR                                                 
#> NA1 NA2            MI     MX   LMIN    LN     H      ID      SC      pP   DE  
1hiv_a POL_HV1H2      57    155     99  0.665  0.099  100.0  103.69   30.00 "POL PROT.." 
1hiv_a POL_HV1BR      69    167     99  0.664  0.098   99.0  103.62   30.00 "POL PROT.. 
<i>... lines skipped ...</i> 
1hiv_a POL_MLVAV       9    102     99  0.648  0.078   27.3   23.41    5.31 "PROTEASE.." 
1hiv_a VPRT_MPMV     172    272     99  0.799  0.290   29.3   21.95    4.82 "PROTEASE.." 
1hiv_a VPRT_SRV1     172    269     99  0.799  0.290   27.3   21.65    4.72 "PROTEASE.." 
1hiv_a GPDA_RABIT     33    145     99  0.785  0.264   28.3   20.98    4.50 "GLYCEROL3P" 

• NA1 - the query sequence (a single command can search several query sequences)
• NA2 - the name of the database sequence
• MI : MX - the matching fragment boundaries in the database sequence
• QMI : QMX - the matching fragment boundaries in the query sequence
• LMIN - the shortest sequence length in a pair (query, database sequence)
• LN - log-correction factor (not used in pP but you may want to use it to resort the table).
• H - the fraction of the database sequence covered by the alignment with the query. If you search against a database of domains this number should be close to 1 (e.g. the hit is less significant if your query is only a part of a domain). It can be taken into account by multiplying pP by this number.
• ID - percent sequence identity (number of identical residue pairs in the alignment divided by LMIN)
• SC - normalized alignment score which is used to calculated the Probability. The score depends on the residue substitution matrix and gap penalties. (see the Score function).
• pP = -log₁₀ ( Probability )
• DE - the database sequence definition

 
 s_searchDB = s_icmhome + "/data/blast/pdbseq"
 read sequence "GTPA_HUMAN.swi"  
 find database s_searchDB output="gtpa1"  
 find database pattern="C?[DN]?\{4\}[FY]?C?C" s_searchDB margin = 5 
 
 unknown1=Sequence("TTCCPSIVARSNFNVCRLPGTPEAICATYTGCIIIPGATCPGDYAN") 
 find database exact unknown1 s_searchDB margin=1 

find database fast [ = i_speed] sequence s_dbFile [output=s_file] [name=s_tabName]

very fast dictionary-based sequence search algorithm. Requires a blast-formated database file. Options:

• fast= i_speed # a number from 1 (slow, rigorous) to 100 (fast and only almost identical sequences).
• output= s_file # saves the output to a file.

Example:

read sequence swiss web "1433B_HUMAN" # read one sequence 
find database fast=90 1433B_HUMAN     # search pdbseq database (the default)

See also: write index sequence command that creates BLAST files from a FASTA file.

find molecule: chemical substructure search

[ find-sstructure | find-molecule-sstructure ]

A family of chemical substructure identification commands:

• find molecule sstructure [tether] [hydrogen] ms1 ms2 [all] # substructure or maximal common substructure, equivalent atom pairs in S_out # all option will add hydrogen # tries different topologically equivalent permutations to find best correspondence.

• prepare the target strings with the Smiles( a_//![hdt]* ) function (exclude hydrogen, deuterium and tritium)
• search the source string made without hydrogens

• i_out - contains the number of hits
• I_out - contains the integer array of the hit numbers

WARNING: This is obsolete way of chemical substructure searching. Use: find table Index chemical other chemical functions

find molecule reverse ms_1 s_smile

WARNING: This is obsolete way of chemical substructure searching. Use find chemical instead.
: find sstructure [minimize]

find maximal common substructure in the input set of chemicals. With the minimize option the command will try to aggregate multiple R-groups into single one (suitable for matched pair analysis)

: find molecule sstructure [ all ] [ tether ] [ hydrogen ]

find maximal common substructure in selected atoms of the two molecules. Without the all option, one largest pair of matching fragments is identified. The pairs of equivalent atoms separated by a vertical bar will be stored in S_out, e.g.

a_C2H6.m/1/c1|a_C2H6O.m/1/c1
a_C2H6.m/1/c2|a_C2H6O.m/1/c2

Options:

• all : finds multiple matching fragments. Takes fragments with number of atoms >= minMCSFragmentSize (3 by default )
• tether : tethers the matching as_molIcmObj2 atoms the equivalent atoms of as_molObj1 . works only for the ICM_type objects (see convert and convertObject )
• hydrogen : adds hydrogen into a mapping. ( May slow down the procedure )

The tether option is useful since once the tethers are established, you can superimpose a_//T according to these tethers, or optimize the molecule with tethers, e.g.

build smiles "C(=CC=C(C1)CN(CCNC2)C2)C=1"
build smiles "C(=CC=C(C1)N(CCNC2)C2)C=1"
ds a_*.
find molecule sstructure all tether a_1. a_2.
superimpose a_      # uses tethers to superimpose a_ on a_1.

find molecule [ tether ] as_subFragmentQuery as_IcmTargetContainingQueryFragment
You can also use the alternative set of arguments and use molecular selections instead of the smiles strings. The atom pairs of as_IcmTargetContainingQueryFragment aligned to each sequential atom of the query molecule will be stored in the S_out array. The atom selection of the target will also be returned in the as_out selection.
The tether option for ICM objects: After the equivalent sets of atoms in two molecules are identified, tethers can imposed pulling atoms of as_IcmMolContainingQueryFragment to the equivalent atoms of passive atoms as_subFragmentQuery . The matching atoms of the second selection as_IcmMolContainingQueryFragment which are pulled by tethers to the as_subFragmentQuery template positions can be superimposed with the minimize "tz" v_positionalVariables command.
Important: unselect the hydrogens to speed up the matching procedure, e.g.

  find molecule a_1.//!h* a_2.//!h*

An example:

 
 build string name="a" "se nter his cooh"   # query template 
 build string name="b" "se nter his trp cooh" # target 
 find molecule a_a./his/cg,nd1,ce1,ne2,cd2,cb,ca,n a_b. tether 
 display as_out xstick # the tethered atoms of the target 
 display a_*. 
 minimize "tz" a_b.//?vt* 
 show Rmsd( a_b.//* )  # will show the RMSD of the equivalent atoms 

• Smiles function
• build smiles
• Index( Xm .. ) family of functions to find matches

find chemical ms_sel s_smarts [all]

Searches using smarts pattern s_smarts in ms_sel. The result (matched atoms) will be stored in as_out With all option it'll find all possible matchings.

Example:

 build smiles "CC1=NN=C(NS(C(C=CC(N)=C2)=C2)(=O)=O)S1" name="sulfamethizole"
 display wire
 find chemical a_ "a" all  # finds all aromatic atoms
 display xstick as_out
 find chemical a_ "[$(N~[a;r6])]" all  # finds nitrogen bonded to 6-member aromatic ring
 display cpk as_out

See also:

• find molecule sstructure
• SMILES/SMARTS description
• ( Xm .. ) family of functions to find (substructure +) matches

find pdb: fragment search

find pdb rs_fragment os_objectWhereToSearch s_3D_align_mask [ s_sequencePattern [ s_SecStructPattern ] ] [ r_RMSD_tolerance]
Find a fragment (e.g. a loop) with certain geometry, sequence and/or secondary structure (see also build loop [ stack ]) . Arguments:

• rs_fragment: the search fragment template
• os_objectWhereToSearch: the other object.
• s_3D_align_mask: marks the residues to be used in the 3D superposition and comparison in terms of r_RMSD_tolerance (see below). The number of 'x's (or 'ON' bits) in the mask must be equal to the query fragment length (it may be discontinuous), while the total mask length should be equal to the found fragment length. For example, if you search for an 11-residue loop with the same geometry of 3-residue ends, but any geometry of the middle part your mask must be "xxx-----xxx". If you want to match geometry of the middle part you would invert the mask: "---xxxxx---", etc.
• s_sequencePattern: Use "*" for any sequence. Otherwise you may use regular expressions, for example: "?A[!P]???$".
• s_SecStructPattern: Use "*" for any secondary structure pattern. Otherwise, specify a regular expression, for example "?HHH___EE[!_]".
• r_RMSD_tolerance: RMSD threshold to accept a fragment as a solution. To avoid time-consuming optimal 3D superposition during the search, distance Rmsd (i.e. root-mean-square deviation between two Ca-atom distance matrices of the compared fragments) is used as a measure of spatial similarity on the preliminary stage of each comparison. However, in the resulting list of hits, collected in SearchSummary string array the optimal 3D superposition coordinate Rmsd is presented. Therefore, RMSDs in the output list may exceed the specified threshold.

 
 read pdb "1crn" 
 read object s_icmhome +  "complex"         # object in which to search 
 find pdb a_1./16:18,20:22 a_2. "xxx----xxx" "V[LIVM]?????G??" "*" 2.5
 print s_out

 
 read sequence "zincFing.seq" 
 find prosite 1znf_m            
 show SITES 

• ^ sequence beginning
• $ sequence ending
• ? one character
• * any number of any characters
• [ACD] alternatives
• [!ACD] all but the specified residues
• char \{ i_min, i_max \} : repetition. E.g. ?\{5,8\} from 5 to 8 of any character.

• number - just report the number of hits instead of reporting each match
• mute - suppress terminal output (used in scripts)
• i_mnHits - (default mnSolutions )
• os_objectWhereToSearch - the target molecular object.
• seq_Name - the target sequence. By default, the search is performed among all currently loaded sequences.
• seqNamePattern - the target sequence name pattern to search through many sequences loaded to the shell.

• s_out - text output of all matches
• i_out - the number of hits
• r_out - the ratio to the random expectation (it r_out>1. it means that the number of hits is larger than the random expectation).

 
 read sequence s_pdbDir + "/derived_data/pdb_seqres.txt"  # all pdb-sequences  
 find pattern "[AG]????GK[ST]"   # search for ATP/GTP-binding sites  
 searchPatternPdb "^[LIVAFM]?\{115,128\}[!P]A$"    
     # ^ : seq.start; ?\{115,128\} from 115 to 128 of any res.; $ : seq.end  

find molcart [sstructure|similarity|exact] table=s_molcartTable [ s_smarts|S_smarts|chemarray ] [r_distCutOff] [only] [stereo] [tautomer] [name=s_resultName] [query=s_SQL_condition] [output=s_molcartTable] [number=i_maxHits] [exclude=s_smarts|S_smarts] [append|delete] [ connection_options ]

Performes chemical search in Molcart database. Connection may be specified by connection_options

Supported search modes are:

• exact : exact match
• sstructure : substructure
• similarity r_dist : find similar compounds with distance cutoff r_threshold (between 0 and 1, e.g. 0.1 for very similar compounds)

Other options:

• append : the search results will be appended to the output table, if it exists.
• delete : the specified output table will be overwritten if it already exists.
• center : performs a K-means clustering of all chemicals in the specified table and selects a representative.
  • number=, or
  • distance=
  • tautomer : tries different tautomer forms in substructure and similarity search.
• query = s_SQL_condition> using existing table columns or on-the-fly built-in functions (e.g. MolPSA) in an sql expression., e.g.

  
  find molcart table="amri" query="MolLogP(t.mol)<2 and MolAtomCount(t.mol)=10"  
     # t is a generic name for all tables
  

  allows one to use the following built-in functions in sql-style expressions (see above) : MolAtomCount, MolFormula, MolHBA, MolHBD, MolLogP, MolLogS, MolMaxFusedRings, MolMaxRingSize, MolMinRingSize, MolNofMol, MolNofRings, MolPSA, MolRotB, MolSmiles, MolVolume, MolWeight, MoldHf . It also allows explicit fields of the specified table to be mentioned as well, e.g. query="t.molid=2345" In SQL allowed logical and comparison operators are and, or not , =, > < ≥ ≤ !=
• output : The output option allows one to save search results in another database table s_molcartTable. It is possible to specify a table in another molcart connection by using "connectionID;database.table" format.

Examples :

  find molcart sstructure table="pub.all" "c1ccccc1" number=1000 name="myHits"  # by substructure
# find by substructure (contains 4 benzene rings)
  find molcart sstructure table="pub.all" "c1ccccc1" query="MolNofRings(t.mol)=4" name="tt"
  find molcart exact table="pub.all" t.mol  # finds exact matches. chemical array pattern
  find molcart similarity 0.2 table="pub.all" "CC1=CN(C(NC1=O)=O)[C@H]1C[C@@H]([C@H](CO)O1)O" 

See also: Index chemical Nof Find find table

find table : chemical search in ICM table

find table {T_table|filename=<s_file} {sstructure [group]|similarity|exact} [ s_smarts|S_smarts|chemarray ] [r_distCutOff] [only] [stereo] [tautomer] [query=s_ICM_condition] [name=s_resultName|select] [index=I_index]] [append]

Performs chemical and text search in the local table. nProc = is supported.

Arguments:

• T_table : input table.
• Alternatively an SDF or CSV s_file may be specified.
• s_smarts or S_smarts chemarray : input pattern
• search type: sstructure similarity exact
• r_distCutOff distance cutoff for similarity search
• With stereo option chirality will be taken into account in substructure and similarity searches.
• With tautomer option different tautomer forms will be tried in the search.
• group option toggles the special search mode when all atoms in the pattern except attachment points are treated "as drawn" (not other attachments are allowed)
• With only option only number of hits will be returned.
• With select option matched rows in the original table will be selected (not result table will be created)
• name=s_resultName result table name (ignored with select option)
• query=s_ICM_condition extra condition. Using this argument you can specify an extra logical condition for the query. Column names, string constants and numnbers can be used: For example : MolWeight<400
• With append option, search results are appended to the result table

Examples :

  group table t Chemical({ "CC(=O)Oc1ccccc1C(O)=O", "CC(Nc1ccc(cc1)O)=O" } ) "mol"
  add column t Mass(t.mol) name="MW"
  find table t query = "MW<160" select  # select rows with molecular weight < 160
  
  cc = Chemical({"CC(=O)Oc1ccccc1C(O)=O","CCCc1c2c(C(NC(c3cc(ccc3OCC)S(N)(=O)=O)=N2)=O)n(C)n1"}) 
  group table t2 cc "mol"
  # compare chemical tables
  find table exact t  t2.mol select   # select rows in t 
  find table exact t2 t.mol  select   # select rows in t2

  find table similarity t  t2.mol select 0.5   
  find table similarity t2 t.mol  select 0.5  

  # Not enough? Let's increase distance cutoff

  find table similarity t  t2.mol select 0.8   
  find table similarity t2 t.mol  select 0.8  

  # this command can also be used to select arbitrary rows in a table
  find table t2 select index = {1 3 5}
  Index( t2 selection )
  

See also: Index chemical Find find molcart SMILES/SMARTS other chemical functions

find pharmacophore : pharmacophore search in ICM table

find pharmacophore as_pharmQuery chemarray3D [all]

Performs a pharmacophore search in chemarray3D using as_pharmQuery.

Example:

read binary s_icmhome + "example_ph4.icb"
find pharmacophore  a_pharma. t_3D.mol

all option allows one to score all possible mapping for each conformation

See also: Rmsd superimpose makePharma

fix

fix vs
fix (exclude from the free variable list) specified variables (such as bond lengths, angles and phases or torsions) in an ICM-object. This operation can be applied to the current object only (use set object os_objectfirst). See also: unfix .
Examples: