[ alignment | all | alpha helix | amber | append | array | atom | axis ]

[ Alignment gap format ]

• extracting a domain (i.e. a certain position range) from an alignment alignment[i1:i2] or alignment[i] or alignment[ I_pos ]
• extracting an alignment of a group of sequences from a larget alignment Align(aliLarge, I_seqNumbers )
• projected alignment: concatenation of two alignments sharing the same sequence. The shared sequence serves as a ruler for merging the two alignments. The alignments can be of arbitrary size and number of sequences. In the simplest case of three sequences a, b, c and alignments ab and bc, the operation ab//bc will create an alignment of three sequences a b c. The function Align(ab//bc,{1,3}) will extract the, so called, projected alignment of a and c through b. Example:

   
    ali1    //    ali2  returns   Projected ali. 
  a VYRWA-W     b FK-WG--KW     a  VYR-WA---W 
  b -FKWGKW     c AKGWAPGKW     b  -FK-WG--KW 
                                c  -AKGWAPGKW 
  

• projecting a numerical property from a sequence to alignment: r property transfer via alignment {Rarray}( R_property,seq_,ali_,r_gapDefault ).
• projecting a numerical property from alignment to a sequence : map aa property to sequence {Rarray}( R_ali,ali_from,seq_|i_seqNumber )

 
  delete sh3 only Fyn 
  delete sh3 only selection 

• Align( seq1n seq2m [ M_nxmPosScores | area ] ) = ali2
• Align( seq3D1 seq3D2 [ distance | superimpose ] ) = ali3D
• Align( [selection] ) = ali2 ; first two (selected) sequences
• Align( ali seq1 seq2 ) = ali2 ; sub-alignment of seq1 vs seq2
• Align( ali I_seqNumbers ) = sub-alignment
• Consensus ( ali [ i_seq| seq ] ) # direct or projected-to-a-sequence consensus string
• Distance( ali [0| 1| exact] )
• Distance( ali1 ali2 [exact] )
• Index( ali [selection| seq ] )
• Index( ali as_ ) = Iarray ; columns indexes
• Matrix( ali [number] )
• Matrix( ali R_26aa_properties )
• Min( ali seq ) # index of the nearest sequence to seq
• Name( ali [alignment] ) # returns names of sequences in alignment [or alignment itself]
• Name( ali seq ) # returns the name of the closest sequence in alignment
• Namex( ali ) # returns the comment
• Nof ( ali ) # number of sequences in it
• Pattern( ali [exact] ) # converts consensus into a pattern like "A?\{2:4\}C"
• Probability( ali2 .. ) # significance
• Profile( ali .. ) # makes profile
• Rarray( ali exact | simple ) # conservation values
• Rarray( R_l ali_l seq_li|i ) # projects real array of length l to a sequence of li, also opposite
• Res( ali seq ) # 3d residues in alignment
• Score( ali [identity|similarity|comp_matrix..] ) # alignment score
• Select( rs ali ) # propagate selection to other objects by alignment
• Sequence( ali ) # returns a 'consensus' chimeric sequence
• Smooth ( ali i_gapExpand ) # expand around gaps
• String ( ali [tree] ) # alignment as text, or Newick tree.
• Table( ali [I_alipos] [number| residue| label] ) # makes a spreadsheet/ICM table
• calcPairSeqIdsFromAli ali l_mode # macro returning pairwise sequence identities from alignment

• align sequence
• append sequence
• find alignment
• linkali ms
• make tree ali_name [ s_epsFile ]
• make sequence ali_range # extract vertical block
• move ali seq [ i_new_seq_pos ] # move sequence up/down
• select ali rs
• set color ali s|i_schema # eg "icm-combo"
• set field ali i_slot:1|2|3 [ R_aliPosValues] [ s_name ]
• set foreground ali # push alignment window to the top
• set site
• set tether ali # use alignment to set tethers, also superimpose etc.

 
 read alignment "globins.msf" 
 list alignments 
 glob_fragment = globins[10:36] 
 show glob_fragment 
 delete alignments 

How to extract a sub-alignment?If you have a large alignment and you want to select a sub-alignment without realigning, use the Align( ali I_indexes ) function. The indexes in term can be returned by the Index( S_name .. ) function if you know the name pattern of interest. Example in which we create an alignment aln and then extract a sub-alignment with a,b,e :

 make sequence 10 20  # makes rangomd sequences and names them a,b,c,..
 align sequence       # creates alignment aln
# preparations finished
 show Index( Name(aln) "[abe]" regexp all)  # indexes of sequences with names matching the expression
 aln_abe = Align(aln, Index( Name(aln) "[abe]" regexp all))

Displaying hidden alignment blocks in GUI.

GUI allows one to define how a hidden block is displayed. Two parameters can be specified directly from the Tools Panel in the alignment window:

1. the "Hidden Block Format can use the following special symbols:
   • %l number of hidden chars
   • %L length of the hidden block
   • %f hidden from
   • %t hidden to
   e.g. " %f .. %t " or " %L "
2. the "Hidden block width" which defines the total length of the hidden section.

 
 write matrix "fil.mat" append 
 read stack "mc12" append 

• iarray - integer array,
• rarray - real array,
• sarray - string array
• parray - pointer array of binary objects (e.g. chemicals, slides, etc.)

parray-constants do not exist, a parray can be created in ICM or read from a file.
Commas are optional unless you have negative elements in integer or real arrays. Array ICM-shell variables can be created by direct assignment: (e.g. a={2, 4, 67, -4} or b={"wow","oops","ouch"} ), read (e.g. read iarray "numb.iar" ), and written to a file (e.g. write numb "numb" ). You can specify a subset of an integer array (e.g. a[2:15]). Besides, there all kinds of operations and functions on the ICM arrays. There are many ways to create an array:

• read an array from a file: read rarray "a.dat"
• create by direct assignment: a={1, -2, 3, 14}
• use arithmetic expressions: a=Sin(Cos(a))*b
• use functions Iarray, Rarray, or Sarray, e.g.: a=Rarray(15, 2.)
• concatenate two elements, e.g.: a=2//3

Arrays ( array ) may appear in ICM shell as a result of the read xml command. The following functions can be applied to arrays to convert them to a specific type

• Tointeger( array )
• Iarray ( array )
• Toreal ( array )
• Rarray ( array )
• String ( array )
• Sarray ( array )
• Table ( array )

Index access to specific arrays (e.g. a={1,2,3,4,5,6} ):

• by number, e.g. a[1], a[3], a[$] (dollar for the last member)
• by range, e.g. a[2:4], a[4:$]
• by integer array, e.g. a[{1,4,6}], or a[3//4//$]

atom

(Greek): indivisible; the smallest particle of a chemical element that can exist alone or in combination.

ICM functions related to atoms:

Here is a recipe on how to create an object with carbons as Z-axis sampling points every Angstrom:

n = 30; z_shift = 15.
build smiles String("C",n)
strip a_ virtual
delete a_//h*
#
mxyz = Matrix(n,3) # x,y,z matrix initiallized 
for i=1,n
  mxyz[i,3]=z_shift + i - 1.
endfor
#
set a_// mxyz  # assign coordinates