processDCD.pl - Revision history

Edit: /* Examples */

2009-08-01T01:21:03Z

Examples

Edit: /* Description */

2009-08-01T01:16:41Z

Description

Edit: /* Options */

2009-08-01T01:15:33Z

Options

Edit: /* Options */

2009-07-29T04:55:56Z

Options

Edit: /* Options */

2009-07-29T04:55:28Z

Options

Edit: /* Description */

2009-07-29T03:46:54Z

Description

Edit: /* Options */

2009-07-29T03:46:14Z

Options

193.50.234.194: /* Options */

2006-08-29T15:21:17Z

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193.50.234.194: /* Options */

2006-08-29T15:20:34Z

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Feig at 14:16, 12 August 2006

2006-08-12T14:16:41Z

New page

__NOTOC__
== Usage ==

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

== Description ==

== Options ==

; -help : usage information

== Examples ==

←Older revision		Revision as of 01:21, 1 August 2009
Line 31:		Line 31:

	== Examples ==		== Examples ==
		+
		+	<mmtsbToolExample cmd="processDCD.pl" set="test1"></mmtsbToolExample>

@@ Line 6: / Line 6: @@
 == Description ==
-Process a trajectory file with custom commands and custom functions.
+Process a CHARMM trajectory file with custom commands and custom functions.
 == Options ==

@@ Line 13: / Line 13: @@
 ; -inx from&#58;to : analyze the specified frame range from trajectory file
 ; -step size : skip the specified number of steps in between frame analyses
-; -multi from&#58;to :
+; -multi from&#58;to : read from multiple DCD files (file name given as template) with indices according to given range of numbers
 ; -apply cmd : each frame will be temporarily converted into a PDB file and analyzed according to the given command
-; -function file :
+; -function file : analyze frames with an internal perl function (see [[analyze.pl]] for more information
 ; -extract name : extract structures and store them as PDB files with a common tag name
 ; -ensdir dir : extract structures into an ensemble with the specified directory name
 ; -ens tag : extract structures into an ensemble with the specified tag name
 ; -rms CA|CAB|C|O|N|side|back|all ... ref : calculate the root mean square deviation of each frame with respect to a reference PDB structure
-; -qscore ref :
+; -qscore ref : calculate Q-score for each frame
-; -boxsize :
+; -boxsize : extract box size information from trajectory
-; -average :
+; -average : calculate average structure from trajectory
 ; -fit ref : fit each frame to the reference
 ; -fitsel cab|ca|cb|heavy : fit each frame with respect to the specified atom selection

@@ Line 26: / Line 26: @@
 ; -fitsel cab|ca|cb|heavy : fit each frame with respect to the specified atom selection
 ; -psf file : use specified protein structure file (PSF)
-; -atoms from:to : use specified atom selection range
+; -atoms from&#58;to : use specified atom selection range
 == Examples ==

@@ Line 11: / Line 11: @@
 ; -help : usage information
-; -inx from:to : analyze the specified frame range from trajectory file
+; -inx from&#58;to : analyze the specified frame range from trajectory file
 ; -step size : skip the specified number of steps in between frame analyses
-; -multi from:to :
+; -multi from&#58;to :
 ; -apply cmd : each frame will be temporarily converted into a PDB file and analyzed according to the given command
 ; -function file :

←Older revision		Revision as of 03:46, 29 July 2009
Line 6:		Line 6:
	== Description ==		== Description ==

		+	Process a trajectory file with custom commands and custom functions.

	== Options ==		== Options ==

←Older revision		Revision as of 03:46, 29 July 2009
Line 10:		Line 10:

	; -help : usage information		; -help : usage information
		+	; -inx from:to : analyze the specified frame range from trajectory file
		+	; -step size : skip the specified number of steps in between frame analyses
		+	; -multi from:to :
		+	; -apply cmd : each frame will be temporarily converted into a PDB file and analyzed according to the given command
		+	; -function file :
		+	; -extract name : extract structures and store them as PDB files with a common tag name
		+	; -ensdir dir : extract structures into an ensemble with the specified directory name
		+	; -ens tag : extract structures into an ensemble with the specified tag name
		+	; -rms CA\|CAB\|C\|O\|N\|side\|back\|all ... ref : calculate the root mean square deviation of each frame with respect to a reference PDB structure
		+	; -qscore ref :
		+	; -boxsize :
		+	; -average :
		+	; -fit ref : fit each frame to the reference
		+	; -fitsel cab\|ca\|cb\|heavy : fit each frame with respect to the specified atom selection
		+	; -psf file : use specified protein structure file (PSF)
		+	; -atoms from:to : use specified atom selection range

	== Examples ==		== Examples ==

←Older revision		Revision as of 15:21, 29 August 2006
Line 10:		Line 10:

	; -help : usage information		; -help : usage information
−	~~--help~~

	== Examples ==		== Examples ==