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Jul 1 2004
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[ autoSavePeriod | defSymGroup | i_out | iProc | maxColorPotential | maxMemory | minTetherWindow | mnSolutions | mncalls | mncallsMC | mnconf | mnhighEnergy | mnreject | mnvisits | nLocalDeformVar | nSsearchStep | nProc | randomSeed | segMinLength | sequenceBlock | sequenceLine | surfaceAccuracy | windowSize ]
Here is the alphabetically sorted dump of integer parameters
defined in the ICM-shell. These parameters are used by various
commands and functions and can be changed interactively, e.g.
mncallsMC= 10000
montecarlo
ICM-shell integer variables are the following.
In the course of a montecarlo or ssearch
procedures which may run for days, the current stack of
conformations which accumulates the best energy representatives of different
conformational areas is saved periodically to allow access to intermediate
results of the simulations. The above parameter defines the number of
stack changes after which it is saved to a disk file.
Set autoSavePeriod to 1 if you want
to be conservative.
If you set autoSavePeriod to 0 , the stack will not be saved at all.
Default (10).
defines a crystal space group number. To find the group name and symmetry
operations use the
Symgroup function.
Default (0) means that the group is not defined.
Examples:
defSymGroup = 19 # direct assignment. You know group 19, don't you?
defSymGroup = Symgroup("P212121") # Oh, you do not! ..
defSymGroup = Symgroup("P61 2 2") # This one you do not remember for sure
an integer where some commands or functions store their integer output:
-
Rmsd saves the number of aligned equivalent points;
-
Srmsd saves the number of aligned equivalent points;
-
convert saves the number of heavy atoms missing from the pdb-template (e.g. atoms
of the flexible lys side-chain are not given in the pdb-file).
-
superimpose
saves number of aligned equivalent points;
-
set tether saves the number of tethers imposed;
-
set drestraint
saves the number of distance restraints imposed;
-
set vrestraint
saves the number of variable restraints imposed;
-
make disulfide bond
saves the number of imposed disulfide bonds;
-
minimize
saves the number of function evaluations;
-
montecarlo
saves the total number of function evaluations during minimization;
-
show area skin
saves the total number of triangles in the Connolly construction.
Default (0).
the current of process number filled by the fork
command. This number is zero for the parent process.
Default (0).
local electrostatic potential in kcal/e.u.charge units at which
the surface element is colored by extreme red or extreme blue.
All higher values will have the same color. This absolute scaling
is convenient to develop a feeling of electrostatic properties of
molecular surfaces.
If the maxColorPotential is set to 0. the the color grob potential
command will perform automated scaling to the absolute maximal value of the
potential.
See also: color grob potential, dsRebel , Potential , make grob potential .
Example:
build string "se glu arg" # dipeptide
maxColorPotential = 3.
dsRebel a_ yes
maxColorPotential = 6.
dsRebel a_ yes
maximal memory size requested by the program in megabytes.
It is used to read blocks of databases in the search commands.
Make sure that this parameter is reasonable.
If your maxMemory is larger than what your computer actually has,
expect serious delays. However, usually computers can handle it
by swapping memory onto disk,
which can be slow.
Recommendation: divide your available RAM by a factor from 2 to 4.
Current memory resources are reported by the chkdsk command on a PC
or by the top command on a UNIX workstation.
Do not forget that ICM itself will additionally allocate some
BufferSpace specified in the icm.cfg file.
Default (10.0) Mb
maximal number of preceding torsions strictly speaking rigid bodies
which are locally minimized during the
chain growth procedure
(the minimize tether command)
to create an ICM-object with ideal geometry
on the basis of a set of arbitrary atom coordinates (ofter referred
to as the regularization procedure).
Default (30).
this parameter limits the number of hits retained by the program
after a search.
It is used in several icm-search functions:
- find molecule - chemical substurcture search
- find pattern - find sequence pattern in sequences of mol. objects.
- find database - advanced sequence similarity search
- align ms_1 ms_2 - alternatives solutions for 3D superposition
- find profile - find protein Prosite profiles in a sequence
- find prosite - find protein Prosite patterns in a sequence
Default (100).
maximal number of function calls in local minimization performed in
minimize,
and as a part of one step of a multistep procedure in
montecarlo,
ssearch,
convert .
The number of function evaluations required to find the local minimum varies
widely depending on the terms used (i.e. the "tz" term makes
minimization very slow, if structure is far from its target).
If the minimum is found according to the
tolGrad
criterion, the procedure will be terminated anyway.
Default (100).
See also: minimizeMethod , tolGrad , drop .
maximal number of function calls in the montecarlo command.
Since the procedure performs random steps
accompanied by local minimization (controlled by the mncalls parameter),
the number of function evaluations for the whole procedure can
be roughly evaluated as a product of mncalls
and the number of MC iterations. mncallsMC should be sufficiently
large to ensure convergence of the global optimization procedure and
may range from 10,000 for a single side-chain, 100,000 for a 3-4 residue
peptide to several million calls for 15-20 residue peptide or a large
protein loop.
Default ( 1000 ).
The default value is small to minimize damage of the unintentional
calls of the montecarlo command.
See also: montecarlo , mncalls .
maximal number of conformations
in the conformational stack .
The stack stops growing after this number is achieved
and starts replacing representative conformations with higher energy values
by new conformations with superior energies, if the latter are found.
Default (50)
See also:
montecarlo , ssearch .
maximal number of consecutive accepted trial conformations which do not
change the conformational
stack
because their energies are higher than energies of the stack conformations.
Therefore, the
montecarlo
procedure is walking in the high energy area and is probably wasting its time.
When this threshold is reached the procedure acts according to the
highEnergyAction
parameter.
Default (50)
See also: mnvisits , mnreject , stack .
maximal number of consecutive rejections (due to the Metropolis criterion)
of trial conformations generated by the
montecarlo
procedure.
When this threshold is reached the procedure acts according to the
rejectAction
parameter (which usually increases the simulation temperature).
Default (10)
See also: mnvisits , mnhighEnergy .
maximal number of visits to the same slot of the conformational
stack
in the course of a
montecarlo
procedure.
When this threshold is reached the MC procedure acts according to the
visitsAction
parameter.
A visit is an event when a newly generated conformation finds
a slot with a similar conformation in it, but the stack conformation
is not replaced by the new one because it has a better energy.
The optimal mnvisits parameter grows with the size of the problem
(it may be several hundred for a 15-20 residue peptide).
Default (50)
See also: mnreject , mnhighEnergy .
Number of backbone torsion angle variables (excluding omegas) which are changed
simultaneously to provide local deformation. This parameter can be less than the
actual number of backbone torsion angles in the loop. In other words it is OK if
the loop contains more than nLocalDeformVar variables, however, if it
contains less than nLocalDeformVar variables, it will not be deformed.
Default (10), minimal number (8).
See also: montecarlo local.
number of steps per variable for ssearch . Normally
the whole [-180., 180.] range is divided into nSsearchStep parts.
In the local mode
(i.e. the search is performed around a particular conformation)
the total search range around each variable is defined by
the ssearchStep parameter (30. deg. by default)
Default (3) .
Number of processors used by the parallel version of the program.
Default (1). Range [1: maximum_number_of_processors_available ].
is a seed used by the random-number generator in the montecarlo , randomize , Random function.
Helpful if you need to reproduce exactly a calculation
which uses random number(s). If the variable has its zero default value,
the random function is seeded from the current time plus the process id.
Otherwise, if you explicitly redefine it before, let us say, a montecarlo run,
it will use the specified number.
Note that the randomSeed parameter can be set only once in the very beginning
of the session. If you redefine its value in the middle of the session, it will
not be used. To push the new value of the seed, use the set randomize i_newRandomSeed
command.
Default (0).
Examples:
randomSeed=2493059372 # this number you took from the previous run
montecarlo # simulation will reproduce the previous one
#
...
#
set randomize 2493059372
montecarlo
secondary structure segments
shorter than this threshold will be ignored when a simplified quantitative
representation of the polypeptide fold is constructed using the
assign sstructure segment command.
Default (3).
length of the contiguous sequence block in sequence output.
Default (10).
See also: sequenceLine .
maximum sequence length printed on each line. Usually sequence is
additionally subdivided into smaller blocks.
The same parameter also controls the size of alignment block
as saved by the write alignment command.
Example:
read alignment s_icmhome+"sh3"
sequenceLine=1000
write sh3 "aaa"
Default (60). Values >= 1 .
See also: sequenceBlock
accuracy level used in surface calculations (not graphics).
By reducing the level, you can speed up the accessibility calculation
in the show area surface command.
The corresponding
number of dots per sphere is the following:
- Level 1 ( 89 dots )
- Level 2 ( 144 dots )
- Level 3 ( 233 dots )
- Level 4 ( 377 dots )
- Level 5 ( 610 dots )
Default (3)
See also: show area surface, "sf" energy term .
number of elements used for sliding window averaging by the
Smooth
function.
Default (7).
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