enslatsim.pl - Revision history

Edit: /* Options */

2009-07-30T13:59:54Z

Options

Edit: /* Description */

2009-07-30T13:54:58Z

Description

Edit: /* Description */

2009-07-30T13:54:46Z

Description

Feig at 14:30, 12 August 2006

2006-08-12T14:30:42Z

New page

__NOTOC__
== Usage ==

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

== Description ==

This script is used to generate structure ensembles from
multiple lattice simulation runs. Many options are similar
to <docmark>latticesim.pl</docmark>, the script for single
lattice simulation runs. 
The ensemble directory can be given with -dir if it is
not the current directory. The number of desired runs is specified
using -run either followed by a single number
for the total number of runs or by an explicit interval. 
During lattice simulations a MONSSTER sequence file is needed
and has to be provided through the -seq if it has
not been given previously and its location is not available
from the ensemble configuration file. A reference PDB file for
comparison with the native conformation may be given through
-natpdb but is not required. For loop or fragment
modeling the range of residues that are being modeled
and a template PDB file with the structure outside the
modeled residues are specified using -l. Like the location
of the sequence file and the native PDB structure this
data may already be present in the ensemble configuration file
and does not need to be given in that case. 
With the -opt one or more option files can be read in.
By default the option file associated with the lat tag
is always read if present. 
The option -keeptraj is available to save the lattice
trajectory files for later analysis. These files are usually not
kept since they require a significant amount of disk space. 
Although this script will work in a serial fashion, one would
probably want to take advantage of parallel architectures for
a larger number of simulations. The parallel options
are explained <A HREF="http://mmtsb.scripps.edu/cgi-bin/parallelopt">here.</A> 
The remaining options are used to control the lattice simulations
and are kept in a file tag.options for later reference
and subsequent executions of this script on the same ensemble set.
They are very similar to the options in
<docmark>latticesim.pl</docmark> where a more detailed explanation
can be found.

== Options ==

; -help : usage information

== Examples ==

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

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

<mmtsbToolExample cmd="enslatsim.pl" set="/apps/mmtsb/bench/enslatsim.pl-test/test3"></mmtsbToolExample>

<mmtsbToolExample cmd="enslatsim.pl" set="/apps/mmtsb/bench/enslatsim.pl-test/test4"></mmtsbToolExample>

@@ Line 15: / Line 15: @@
 using <B>-run</B> either followed by a single number
 for the total number of runs or by an explicit interval.<BR>
 During lattice simulations a MONSSTER sequence file is needed
 and has to be provided through the <B>-seq</B> if it has

@@ Line 8: / Line 8: @@
 This script is used to generate structure ensembles from
 multiple lattice simulation runs. Many options are similar
-to <docmark>latticesim.pl</docmark>, the script for single
+to [[latticesim.pl]], the script for single
-lattice simulation runs.<BR><BR>
+lattice simulation runs.<BR>
 The ensemble directory can be given with <B>-dir</B> if it is
 not the current directory. The number of desired runs is specified
@@ Line 28: / Line 29: @@
 With the <B>-opt</B> one or more option files can be read in.
 By default the option file associated with the <font color=#508060>lat</font> tag
-is always read if present.<BR><BR>
+is always read if present.<BR>
 The option <B>-keeptraj</B> is available to save the lattice
 trajectory files for later analysis. These files are usually not
@@ Line 35: / Line 37: @@
 probably want to take advantage of parallel architectures for
 a larger number of simulations. The parallel options
-are explained <A HREF="http://mmtsb.scripps.edu/cgi-bin/parallelopt">here.</A><BR>
+are explained [http://feig.bch.msu.edu/mmtsb/PARALLELoptions here]<BR>
 The remaining options are used to control the lattice simulations
 and are kept in a file <font color=#508060>tag.options</font> for later reference
 and subsequent executions of this script on the same ensemble set.
 They are very similar to the options in
-<docmark>latticesim.pl</docmark> where a more detailed explanation
+[[latticesim.pl]] where a more detailed explanation
 can be found.
 == Options ==

@@ Line 50: / Line 50: @@
 ; -help : usage information
+; -seq file : provide MONSSTER sequence file
 == Examples ==