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Jul 1 2004
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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_warn | l_wrapLine | l_writeStartObjMC | l_xrUseHydrogen ]
ICM-shell logical variables are the following.
if yes, invokes antialising for lines displayed in the graphics window.
This feature is not supported on all the platforms.
Default ( no ).
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 ).
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 ).
if yes, break too the
ribbon if the distance between
the reference atoms is larger than 9 Angstroms.
Default ( yes ).
if no, suppresses paging in the output of ICM commands.
Useful in batch jobs.
Default ( yes ).
if yes, print some debug information
Default ( no ).
active in most commands and functions using string comparisons.
Default ( no ).
if no, do not show commands in batch mode
Default ( yes ).
if no, overwrite the contents of an existing file; ask permission to
overwrite it otherwise.
Default ( no ).
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 ).
if yes, print info messages
Default ( yes ).
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.
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,`readmol{read mol}, read mol2, build smiles
and set bond auto.
a logical variable similar to i_out and r_out .
Default ( yes ).
if yes, show
print
command with arguments as well as the result of its action.
Default ( no ).
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
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 convertion 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 to keep acidic groups unchanged and uncharged.
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_m
Default ( yes ).
display one-line info about each Monte Carlo trial conformation.
Default ( yes ).
display every step of the local minimization procedure.
Default ( no ).
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.
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 ).
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 ).
show the secondary structure string assigned to a sequence
in the commands show sequence, show alignment,
write alignment.
Default ( no ).
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 ).
Obsolete. Now you can achieve the same via s_icmPrompt variable.
Examples:
s_icmPrompt = "icm/%o/%e> " # equivalent to l_showTerms=yes
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 ).
wrap long lines if yes. If no truncate long lines
and add a dollar sign ($) to indicate that truncation has occurred.
Default ( yes ).
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 ).
defines whether hydrogen atoms are used in calculations of crystallographic
structure factors from atom coordinates (the term).
Default ( yes ).
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