MMTSB
Tool Set Documentation

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
<docmark>vicinity.pl</docmark> but in addition automatically
+
[[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
<docmark>vicinity.pl</docmark>.<BR>
+
[[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
<docmark>ensmin.pl</docmark> using the <B>-opt</B> parameter.<BR>
+
[[ensmin.pl]] using the <B>-opt</B> parameter.<BR>
 +
 
 
== Options ==
 
== Options ==
  
 
; -help : usage information
 
; -help : usage information
 
+
; -dir directory : data directory
 +
; -run [from&#58;]to : limit to subset of ensemble
 +
; -opt file[&#58;file...] : read options from file
 +
; -l min&#58;max[=...] : residues around which rest of structure is cut out
 +
; -hard value[&#58;force] : outer cutoff radius and force constant
 +
; -soft value[&#58;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]]

Show source


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.