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Difference between revisions of "enscut.pl"
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to consider only the surrounding local protein environment. | to consider only the surrounding local protein environment. | ||
It shares some of the options and functionality with | It shares some of the options and functionality with | ||
| − | + | [[vicinity.pl]] but in addition automatically | |
considers all ensemble structures and generates a new set of | considers all ensemble structures and generates a new set of | ||
reduced structures.<BR> | reduced structures.<BR> | ||
| + | |||
Required parameters are input and output tags and the | Required parameters are input and output tags and the | ||
definition of the loop or fragment residues with <B>-l</B> | definition of the loop or fragment residues with <B>-l</B> | ||
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<B>-run</B>. The <B>-hard</B> and <B>-soft</B> | <B>-run</B>. The <B>-hard</B> and <B>-soft</B> | ||
options are equivalent to the same options in | options are equivalent to the same options in | ||
| − | + | [[vicinity.pl]].<BR> | |
| + | |||
The resulting restraint definition to be used in subsequent | The resulting restraint definition to be used in subsequent | ||
simulation or minimization runs is written to the options | simulation or minimization runs is written to the options | ||
file of the output tag which may be read in later, e.g. by | file of the output tag which may be read in later, e.g. by | ||
| − | + | [[ensmin.pl]] using the <B>-opt</B> parameter.<BR> | |
| + | |||
== Options == | == Options == | ||
; -help : usage information | ; -help : usage information | ||
| − | + | ; -dir directory : data directory | |
| + | ; -run [from:]to : limit to subset of ensemble | ||
| + | ; -opt file[:file...] : read options from file | ||
| + | ; -l min:max[=...] : residues around which rest of structure is cut out | ||
| + | ; -hard value[:force] : outer cutoff radius and force constant | ||
| + | ; -soft value[:force] : inner cutoff radius and force constant | ||
== Examples == | == Examples == | ||
<mmtsbToolExample cmd="enscut.pl" set="/apps/mmtsb/bench/enscut.pl-test/test1"></mmtsbToolExample> | <mmtsbToolExample cmd="enscut.pl" set="/apps/mmtsb/bench/enscut.pl-test/test1"></mmtsbToolExample> | ||
Latest revision as of 14:18, 30 July 2009
Usage
usage: enscut.pl [options] intag outtag
options: [-dir workdir]
[-run [from:]to]
[-opt file[:file]]
[-l min:max[=min:max=...]]
[-hard value[:force]]
[-soft value[:force]]
Description
This script is used to cut out parts of a protein in ensemble
structures for loop or fragment modeling where it may be sufficient
to consider only the surrounding local protein environment.
It shares some of the options and functionality with
vicinity.pl but in addition automatically
considers all ensemble structures and generates a new set of
reduced structures.
Required parameters are input and output tags and the
definition of the loop or fragment residues with -l
unless the fragment residues have been previously stored in
the ensemble configuration file.
Options may be used to provide the ensemble directory with
-dir and select a subset of available structures with
-run. The -hard and -soft
options are equivalent to the same options in
vicinity.pl.
The resulting restraint definition to be used in subsequent
simulation or minimization runs is written to the options
file of the output tag which may be read in later, e.g. by
ensmin.pl using the -opt parameter.
Options
- -help
- usage information
- -dir directory
- data directory
- -run [from:]to
- limit to subset of ensemble
- -opt file[:file...]
- read options from file
- -l min:max[=...]
- residues around which rest of structure is cut out
- -hard value[:force]
- outer cutoff radius and force constant
- -soft value[:force]
- inner cutoff radius and force constant
Examples
enscut.pl -dir data -l 34:41 -hard 14:5.0 -soft 10:1.0 whole lim
cuts out a protein fragment around the loop at residues 34 through 41 from
all ensemble structures associated with the whole tag. The
resulting PDB structure is stored under the tag lim.
The residue cutoff is set to 14 A, a soft cutoff of 10 A is set to
determine the residues for which weaker restraints are applied. The
force constants for the restraints are set to 5 and 1 kcal/mol,
respectively. The restraint definition is stored in the ensemble
options file for subsequent minimization or simulation runs.