genrestr.pl - Revision history

Edit: /* Options */

2009-07-29T02:47:55Z

Options

Edit: /* Options */

2009-07-29T02:47:03Z

Options

Edit: /* Description */

2009-07-29T02:45:18Z

Description

Edit: /* Description */

2009-07-29T02:45:10Z

Description

Feig at 14:21, 12 August 2006

2006-08-12T14:21:28Z

New page

__NOTOC__
== Usage ==

<mmtsbToolUsage cmd="genrestr.pl"></mmtsbToolUsage>

== Description ==

Generates a positional restraint file for use with MONSSTER.
The restraints can be specified either explicitly with -r
or implicitly with -l. The -r option is followed
by a list of residue ranges with a force constant. This list is
translated directly into the corresponding restraint file. 
The option -l is more useful for loop and fragment
modeling. It requires the the maximum force constant and
a list of residues that are not supposed to be restrained
as arguments. Using these parameters restraints for
the other residues are generates with force constants that
increase smoothly from the beginning and end of the unrestrained
regions as well as the beginning and end of the whole sequence.
A MONSSTER sequence file has to be provided with -seq
when the option -l is used. It may also be given with
the -r option for translating the residue numbering
accordingly.
== Options ==

; -help : usage information

== Examples ==

<mmtsbToolExample cmd="genrestr.pl" set="/apps/mmtsb/bench/genrestr.pl-test/test1"></mmtsbToolExample>

<mmtsbToolExample cmd="genrestr.pl" set="/apps/mmtsb/bench/genrestr.pl-test/test2"></mmtsbToolExample>

@@ Line 10: / Line 10: @@
 or implicitly with <B>-l</B>. The <B>-r</B> option is followed
 by a list of residue ranges with a force constant. This list is
-translated directly into the corresponding restraint file.<BR><BR>
+translated directly into the corresponding restraint file.<BR>
 The option <B>-l</B> is more useful for loop and fragment

@@ Line 10: / Line 10: @@
 or implicitly with <B>-l</B>. The <B>-r</B> option is followed
 by a list of residue ranges with a force constant. This list is
-translated directly into the corresponding restraint file.<BR>
+translated directly into the corresponding restraint file.<BR><BR>
 The option <B>-l</B> is more useful for loop and fragment
 modeling. It requires the the maximum force constant and
@@ Line 22: / Line 23: @@
 the <B>-r</B> option for translating the residue numbering
 accordingly.
 == Options ==

@@ Line 28: / Line 28: @@
 ; -help : usage information
 ; -r min&#58;max_force[=...] : generate harmonic restraint force for given residue range with given force constant
 == Examples ==