rexanalysis.pl - Revision history

Edit: /* Examples */

2009-07-31T01:52:46Z

Examples

2009-07-31T01:39:35Z

Examples

2009-07-30T22:11:03Z

Examples

2009-07-30T22:10:14Z

Examples

2009-07-30T21:44:02Z

Description

2009-07-30T21:43:20Z

Options

2009-07-30T21:41:37Z

Description

2009-07-30T21:37:27Z

Description

2009-07-30T21:36:15Z

Description

2009-07-29T15:58:26Z

Description

←Older revision		Revision as of 01:52, 31 July 2009
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	<mmtsbToolExample cmd="rexanalysis.pl" set="test3"></mmtsbToolExample>		<mmtsbToolExample cmd="rexanalysis.pl" set="test3"></mmtsbToolExample>
−
−	~~<mmtsbToolExample cmd="rexanalysis.pl" set="test4"></mmtsbToolExample>~~
−
−	~~<small><span style="color:#800000">rexanalysis.pl -inx 1500:2000 -bycond 2 -nsel B:1. -out traj.dcd -verbose</span></small>~~
−	<br>This command directly extracts all PDB structures that are within the 1500 to 2000 frame range and simulated under condition 2 and stores them into a CHARMM compatible trajectory file. The selection stores only chain B, residue 1 coordinates. The verbose option prints out additional information to STDOUT as each frame is being processed.

@@ Line 47: / Line 47: @@
 <mmtsbToolExample cmd="rexanalysis.pl" set="test4"></mmtsbToolExample>
 <small><span style="color:#800000">rexanalysis.pl -inx 1500:2000 -bycond 2 -nsel B:1. -out traj.dcd -verbose</span></small>
 <br>This command directly extracts all PDB structures that are within the 1500 to 2000 frame range and simulated under condition 2 and stores them into a CHARMM compatible trajectory file.  The selection stores only chain B, residue 1 coordinates.  The verbose option prints out additional information to STDOUT as each frame is being processed.

@@ Line 42: / Line 42: @@
 <mmtsbToolExample cmd="rexanalysis.pl" set="test1"></mmtsbToolExample>
-<small><span style="color:#800000">rexanalysis.pl -inx 1500:2000 -bytemp 310 -apply "convpdb.pl -chain A |  centerOfMass.pl " > centerOfMass-A-temp310.data</span></small>
+<mmtsbToolExample cmd="rexanalysis.pl" set="test2"></mmtsbToolExample>
-  add output
+<mmtsbToolExample cmd="rexanalysis.pl" set="test3"></mmtsbToolExample>
 <small><span style="color:#800000">rexanalysis.pl -inx 1500:2000 -best -apply "convpdb.pl -chain A |  centerOfMass.pl " > centerOfMass-A-cond0.data</span></small>

←Older revision		Revision as of 22:10, 30 July 2009
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	== Examples ==		== Examples ==
		+
		+	<mmtsbToolExample cmd="rexanalysis.pl" set="test1"></mmtsbToolExample>

	<small><span style="color:#800000">rexanalysis.pl -inx 1500:2000 -bytemp 310 -apply "convpdb.pl -chain A \| centerOfMass.pl " > centerOfMass-A-temp310.data</span></small>		<small><span style="color:#800000">rexanalysis.pl -inx 1500:2000 -bytemp 310 -apply "convpdb.pl -chain A \| centerOfMass.pl " > centerOfMass-A-temp310.data</span></small>

@@ Line 15: / Line 15: @@
 program by using the <TT>-wham</TT> option.<BR>
-When it is desirable to deal with trajectory files rather than archive files, <TT>-out</TT> can be used to specify a CHARMM-compatible trajectory output file where structures will be written.  This option for generating a DCD file is useful when dealing with large structures, for visualization, and for analysis.  A subset of coordinates can be written to the trajectory file via the <TT>-atoms</b> or <TT>-nsel</TT> options.
+When it is desirable to deal with trajectory files rather than archive files, <TT>-out</TT> can be used to specify a CHARMM-compatible trajectory output file where structures will be written.  This option for generating a DCD file is useful when dealing with large structures, for visualization, and for analysis.  A subset of coordinates can be written to the trajectory file via the <TT>-atoms</TT> or <TT>-nsel</TT> options.
 == Options ==

@@ Line 26: / Line 26: @@
 ; -bytemp temp : show information for specific temperature
 ; -bycond condindex : show information for specific condition
-; -order client|temp :
+; -order client|temp : when showing information for all clients order either by client or by temperature
 ; -apply cmd : apply a custom command for analysis
 ; -function file : apply a custom function for analysis
 ; -nanvalue value : replace all NAN values with the given value
-; -wham prop&#58;fname&#58;from&#58;to&#58;nbins[=...] : WHAM analysis
+; -wham prop&#58;fname&#58;from&#58;to&#58;nbins[=...] : request WHAM analysis
-; -whamtemp temp[&#58;temp2...] : Temperature-WHAM analysis
+; -whamtemp temp[&#58;temp2...] : specify temperature(s) for WHAM analysis
-; -whamener file :
+; -whamener file : output file name for WHAM energies
 ; -out dcdfile : convert a any archive file to trajectory file
 ; -atoms from&#58;to : specify an atom selection range for output trajectory file

@@ Line 5: / Line 5: @@
 == Description ==
-This script is used to extract and process replica exchange simulation information from the server output files.
+This script is used to extract and process replica exchange simulation information from the server output files.<BR>
-When it is desirable to deal with trajectory files rather than archive files, <b>-out</b> can be used to specify a CHARMM-compatible trajectory output file where structures will be written.  This option for generating a DCD file is useful when dealing with large structures, for visualization, and for analysis.  A subset of coordinates can be written to the trajectory file via the <b>-atoms</b> or <b>-nsel</b> options.
+The option <TT>-byclient</TT> selects simulation information at each step for a specific client. With <TT>-bytemp</TT> and <TT>-bycond</TT> the same information is selected at each step for different replicas at specific temperatures or conditions.<BR>
 == Options ==

@@ Line 6: / Line 6: @@
 == Description ==
 This script is used to extract and process replica exchange simulation information from the server output files.
-With the option -clients a list of all client IDs is selected, with -conds all replica conditions are selected.
+With the option <TT>-clients</TT> a list of all client IDs is selected, with -conds all replica conditions are selected.
-The option -byclient selects simulation information at each step and writes out in the order of the client numbers.
+The option -byclient selects simulation information at each step for a specific client. With -bytemp and -bycond the same information is selected at each step for different replicas at specific temperatures or conditions. <TT>-best</TT> is available as a shortcut notation for the first condition (usually corresponding to the lowest temperature).
 The option -apply can be used to request additional processing with other MMTSB tools. The option -function can be used to further process the data with user-defined functions.