TLSMD - Revision history

Christoph at 00:36, 13 July 2012

2012-07-13T00:36:35Z

Christoph at 19:18, 31 March 2012

2012-03-31T19:18:54Z

Christoph: /* External links */

2012-02-18T18:01:50Z

‎External links

Christoph at 06:51, 12 November 2009

2009-11-12T06:51:16Z

Christoph at 06:45, 12 November 2009

2009-11-12T06:45:27Z

Christoph: /* External links */

2009-11-06T23:47:44Z

‎External links

Christoph: /* Analysis */

2009-08-03T19:26:16Z

‎Analysis

Christoph: /* Analysis */

2009-08-03T18:58:39Z

‎Analysis

Christoph: /* Analysis */

2009-08-03T17:18:06Z

‎Analysis

Christoph: /* See also */

2009-08-03T16:48:47Z

‎See also

@@ Line 1: / Line 1: @@
 '''TLS Motion Determination''' ('''TLSMD''') analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions.<ref name="Painter2006a">Painter J, Merritt EA (2006). "[http://skuld.bmsc.washington.edu/~tlsmd/Acta_D62_439.pdf Optimal description of a protein structure in terms of multiple groups undergoing TLS motion]". ''Acta Cryst, D62(4):439-450''. {{doi|10.1107/S0907444906005270}}.</ref><ref name="Painter2006b">Painter J, Merritt EA (2006). "[http://skuld.bmsc.washington.edu/~tlsmd/JApplCryst_39_109.pdf TLSMD web server for the generation of multi-group TLS models]". ''J Appl Cryst, 39(1):109-111''. {{doi|10.1107/S0021889805038987}}</ref> It does this by partitioning the protein chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a specified maximum number of TLS groups. Each trial partition is evaluated by how well it predicts the observed atomic displacement parameters (ADPs, "thermal parameters") that came out of crystallographic refinement.
 <blockquote>'''Note''':<br/>
@@ Line 183: / Line 185: @@
 ==See also==
 *[[Python Macromolecular Library]] (mmLib)
 ===Analysis===
 *[http://www.hmc.psu.edu/xraycore/secure/ccp4/tlsanl.html TLSANL] &mdash; analysis of TLS tensors and derived anisotropic U factors (part of [[:Category:Ccp4|CCP4]])
@@ Line 200: / Line 204: @@
 ==References==
 <references/>
 ==External links==
 *[http://skuld.bmsc.washington.edu/~tlsmd/ TLS Motion Determination webserver]

@@ Line 2: / Line 2: @@
 <blockquote>'''Note''':<br/>
 On 2009-06-19, we released version 1.3.0 of '''tlsmd'''.<br/>
 On 2008-02-15, we released version 1.0.0 of '''tlsmd'''.<br/>
 On 2008-02-15, we released version 1.1.0 of '''pymmlib'''.<br/>
 On 2007-04-28, we released version 1.0.0 of '''pymmlib'''.<br/>
@@ Line 125: / Line 127: @@
 ==pymmlib installation==
 ===Build===
 Before you build/install anything, check the following file for the correct settings (e.g., correct paths):

← Older revision		Revision as of 18:01, 18 February 2012
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	[[Category:Crystallography]]		[[Category:Crystallography]]
		+	[[Category:Portfolio]]

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 On 2008-02-15, we released version 1.0.0 of '''tlsmd'''.<br/>
 On 2008-02-15, we released version 1.1.0 of '''pymmlib'''.<br/>
 They are both available for download on [http://pymmlib.svn.sourceforge.net/viewvc/pymmlib/ sourceforge].</blockquote>

@@ Line 1: / Line 1: @@
 '''TLS Motion Determination''' ('''TLSMD''') analyzes a protein crystal structure for evidence of flexibility, e.g. local or inter-domain motions.<ref name="Painter2006a">Painter J, Merritt EA (2006). "[http://skuld.bmsc.washington.edu/~tlsmd/Acta_D62_439.pdf Optimal description of a protein structure in terms of multiple groups undergoing TLS motion]". ''Acta Cryst, D62(4):439-450''. {{doi|10.1107/S0907444906005270}}.</ref><ref name="Painter2006b">Painter J, Merritt EA (2006). "[http://skuld.bmsc.washington.edu/~tlsmd/JApplCryst_39_109.pdf TLSMD web server for the generation of multi-group TLS models]". ''J Appl Cryst, 39(1):109-111''. {{doi|10.1107/S0021889805038987}}</ref> It does this by partitioning the protein chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a specified maximum number of TLS groups. Each trial partition is evaluated by how well it predicts the observed atomic displacement parameters (ADPs, "thermal parameters") that came out of crystallographic refinement.
-<blockquote>'''Note''': On 2008-02-15, we released versions 1.1.0 of '''pymmlib''' and 1.0.0 of '''tlsmd'''. They are both available for download on [http://pymmlib.svn.sourceforge.net/viewvc/pymmlib/ sourceforge].</blockquote>
+<blockquote>'''Note''':<br/>
 ==Description==

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 *[http://skuld.bmsc.washington.edu/~tlsmd/ TLS Motion Determination webserver]
 *[http://www.ohloh.net/projects/12891 ohloh - project and code analysis]
 [[Category:Crystallography]]

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 *[http://www.hmc.psu.edu/xraycore/secure/ccp4/tlsanl.html TLSANL] &mdash; analysis of TLS tensors and derived anisotropic U factors (part of [[:Category:Ccp4|CCP4]])
 *[http://www.hmc.psu.edu/xraycore/secure/ccp4/anisoanl.html ANISOANL] &mdash; analyses of anisotropic displacement parameters (part of [[:Category:Ccp4|CCP4]])
-*[http://skuld.bmsc.washington.edu/parvati/parvati.html PARVATI] (Protein Anisotropic Refinement Validation and Analysis Tool)
+*[http://skuld.bmsc.washington.edu/parvati/ PARVATI] (Protein Anisotropic Refinement Validation and Analysis Tool)
 *[http://www.sys.uea.ac.uk/dyndom/dyndomMain.do DynDom] &mdash; a program to determine domains, hinge axes, and hinge bending residues in proteins where two conformations are available.
 *[http://schneider.group.ifom-ieo-campus.it/escet/index.html ESCET] &mdash; a script driven program to analyse and compare three-dimensional protein structures

@@ Line 169: / Line 169: @@
 *[http://www.sys.uea.ac.uk/dyndom/dyndomMain.do DynDom] &mdash; a program to determine domains, hinge axes, and hinge bending residues in proteins where two conformations are available.
 *[http://schneider.group.ifom-ieo-campus.it/escet/index.html ESCET] &mdash; a script driven program to analyse and compare three-dimensional protein structures
 ===Movement===
 *[http://molmovdb.org/ molmovdb.org] &mdash; a database of macromolecular movements with associated tools for flexibility and geometric analysis