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Jun 5 2024
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[ l_antiAlias | l_autoLink | l_bpmc | l_breakRibbon | l_bufferedOutput | l_bug | l_caseSensitivity | l_commands | l_confirm | l_easyRotate | l_info | l_minRedraw | l_neutralAcids | l_out | l_print | l_racemicMC | l_readMolArom | l_showAccessibility | l_showMC | l_showMinSteps | l_showResCodeInSelection | l_showSpecialChar | l_showSites | l_showSstructure | l_showWater | l_showTerms | l_updateLists | l_warn | l_wrapLine | l_writeStartObjMC | l_xrUseHydrogen ]
ICM-shell logical variables are the following.l_antiAlias |
if yes, invokes anti-aliasing for lines displayed in the graphics window. This feature is not supported on all the platforms.
Default ( no ).
l_autoLink |
if yes, tries to link molecules and alignments/sequences automatically. In case of degeneracy, i.e. identical sequences exist with different names, a molecule can be linked to two different alignments containing its sequence etc., the autolink procedure chooses the first occurrence. Use the link command to impose links explicitly, and the show link command to see them. Links can be used by the following commands and functions:
Default ( yes ).
l_bpmc |
if yes, use Biased Probability Monte Carlo moves in the Monte Carlo procedure. See Abagyan and Totrov, 1994 for reference. Important: the probability zones are described in the icm.rst file and should be assigned to a peptide before the montecarlo command with the
set vrestraint a_/*
command.
Default ( yes ).
l_breakRibbon |
if yes, break too the ribbon if the distance between the reference atoms is larger than GRAPHICS.ribbonGapDistance
Default ( yes ).
See also: Select( as error ) function
l_bufferedOutput |
if no, suppresses pagination in the output of ICM commands (including the show command). Useful in batch jobs.
Default ( yes ).
l_bug |
if yes, print some debug information
Default ( no ).
l_caseSensitivity |
active in most commands and functions using string comparisons.
Default ( no ).
l_commands |
if no, do not show commands in batch mode
Default ( yes ).
l_confirm |
if no, overwrite the contents of an existing file; ask permission to overwrite it otherwise.
Default ( no ).
l_easyRotate |
allows faster handling of images in the graphics window. If yes, then the currently displayed solid representations (e.g., ribbon, skin, cpk, etc.) are temporarily hidden if an operation like rotation or translation is undertaken. Only the wire representation remains allowing quick manipulation with the object in use. The previous type of display is restored when rotation or translation is completed. The parameter can be toggled by a keystroke if you assign the l_easyRotate = !l_easyRotate with the set key command.
Default ( no ).
l_info |
if yes, print info messages
The default value is yes.
l_minRedraw |
if no, suppresses redrawing of a displayed structure at each minimization step. The new minimized structure will be redrawn only at the end of minimization. Useful when the graphics is slow or the structure is heavy.
l_neutralAcids |
Several commands such as read mol, read mol2, build smiles and set bond auto include automated assignment of aromatic systems as well as some resonance structures in O-C=O, O-S=O, PO3, O-N=O, and NO3. The automated conversion invoked with the l_readMolArom variable set to yes reassigns the bonds in the group to be equivalent. For the acidic groups it leads to the charged form with two partial charges of -1/2 or -1/3. If you want to suppress this transformation for the CO2,SO2 and PO3 groups only set the l_neutralAcids flag to yes . In this case the acidic groups will be kept unchanged.
Example:
l_neutralAcids = yes read mol s_icmhome+"ex_mol.mol" wireStyle=2 display only a_ # the acidic group is uncharged build hydrogen
Default ( no ).
See also: l_readMolArom,`read-mol{read mol}, read mol2, build smiles and set bond auto.
l_out |
a logical variable similar to i_out and r_out .
Default ( yes ).
l_print |
if yes, show print command with arguments as well as the result of its action.
Default ( no ).
l_racemicMC |
Activate switching between stereoisomers at chiral centers during montecarlo . This flag can also be dynamically activated with the chiral option of the montecarlo command. To reset the chirality status of an atom use the set chiral command
Example:
build string "se nter his cter" set chiral a_/his/ca 3 # set chirality flag to 3 (means a racemic mixture) unfix V_//FC # unfix phases for stereoisomeric rearrangements compare a_//* vicinity = 1. l_racemicMC = yes montecarlo v_//!?vt* # will switch between stereoisomers display display atom label type=6 # to see the isomers # now you can browse the stack solutions
l_readMolArom |
if yes, automatically assigns aromatic rings and resonant structures (CO2,SO2,PO3,NO2,NO3) from patterns of single and double bonds upon reading objects, mol and mol2 files or build from smiles. The automated assignment module is also called by the set bond auto command.
If this flag is set to no , the build hydrogen command will have problems with resonant structures, such as carboxyl groups, - a hydrogen will be attached to the oxygen connected with a single bond to the carbon.
Example of a recommended best conversion procedure for chemical library files:
l_readMolArom = yes # it is the default, but just in case # you also want to use l_neutralAcids = yes read mol s_icmhome + "ex_mol" for i=1,Nof(object) build hydrogens # may have problems if l_readMolArom = no set type mmff # also improves the aromatic system assignment set charge mmff convert # makes an ICM object endfor
Default ( yes ).
See also: l_neutralAcids which allows one to keep acidic groups unchanged and uncharged.
l_showAccessibility |
show the residue accessibility string assigned to a sequence generated from a three dimensional structure in the commands show sequence , show alignment, write alignment . The relative residue accessible area is expressed by an integer number in a scale from 0 to 9 (0-fully buried, 9-fully exposed). Example:
read pdb "1crn" show surface area # calculate atomic and residue accessibilities make sequence a_1 # generate a sequence l_showAccessibility=yes show 1crn_mDefault ( yes ).
l_showMC |
display one-line info about each Monte Carlo trial conformation.
Default ( yes ).
l_showMinSteps |
display every step of the local minimization procedure.
Default ( no ).
l_showResCodeInSelection |
if yes, shows one-letter code for amino-acid residues in residue selections, e.g. a_/^F12:^A23 instead of a_/12:23 . The amino-acid code is preceded by a caret symbol ^. In versions older than 3.1 the amino-acid code was not shown.
l_showSpecialChar |
if yes, displays unprintable characters with the show string and list string commands in text format (like \a \t \n). This flag does not apply to the print command.
Default ( no ).
l_showSites |
show the site string assigned to a sequence in the commands show sequence, show alignment, write alignment. The one-letter site codes are given below.
Default ( yes ).
l_showSstructure |
show the secondary structure string assigned to a sequence in the commands show sequence, show alignment, write alignment.
Default ( no ).
l_showWater |
if yes, all water molecules are shown in the output of commands such as show molecule or show a_* . Set it to no to skip the usually long lists of water molecules in PDB structures.
Default ( yes ).
l_showTerms |
Obsolete. Now you can achieve the same via s_icmPrompt variable.
Examples:
s_icmPrompt = "icm/%o/%e> " # equivalent to l_showTerms=yes
l_updateLists |
if yes, updates the atomic interaction lists during minimization once the maximal displacement reaches listUpdateThreshold . The interaction lists are lists of atom pairs involved in van der Waals, electrostatic or hydrogen bonding interactions and within the vwCutoff or hbCutoff distance. If this parameter is set to no , the lists are not recalculated. To trigger a recalculation, use the
delete listcommand.
Default ( yes ).
l_warn |
if yes, print warning messages. If you want to see warning messages (i.e. l_warn = yes ), but suppress some of the messages, use the s_skipMessages variable (e.g. s_skipMessages = "[147][148]" ) .
Default ( yes ).
l_wrapLine |
wrap long lines if yes. If no truncate long lines and add a dollar sign ($) to indicate that truncation has occurred.
Default ( yes ).
l_writeStartObjMC |
write the starting object in the montecarlo command to a file. This object will have the same fixation (set of free and fixed variables) as in your montecarlo simulation. In case the variable is set to no, the same object can be generated if you repeat the fix and unfix command as in your simulation script.
Default ( yes ).
l_xrUseHydrogen |
defines whether hydrogen atoms are used in calculations of crystallographic structure factors from atom coordinates (the term).
Default ( yes ).
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