Anisotropic refinement - Revision history

Wayne Decatur at 02:12, 27 November 2014

Wayne Decatur — Thu, 27 Nov 2014 02:12:18 GMT

←Older revision		Revision as of 02:12, 27 November 2014
Line 17:		Line 17:
	==Some PDB entries that include ANISOU records==		==Some PDB entries that include ANISOU records==
	* [[3kg2]]		* [[3kg2]]
		+	* [[4un3]], [[4un4]], and [[4un5]]

	==Related==		==Related==

Eric Martz: /* Analysis */

Eric Martz — Sat, 23 Apr 2011 00:57:29 GMT

Analysis

←Older revision		Revision as of 00:57, 23 April 2011
Line 3:		Line 3:
	==Analysis==		==Analysis==
	[http://skuld.bmsc.washington.edu/parvati/parvati.html PARVATI] - Protein Anisotropic Refinement Validation and Analysis Tool.		[http://skuld.bmsc.washington.edu/parvati/parvati.html PARVATI] - Protein Anisotropic Refinement Validation and Analysis Tool.
-	The PARVATI server accepts a PDB file containing ANISOU records or TLS records.
-
-
	The PARVATI server accepts a PDB file containing ANISOU records or TLS records.		The PARVATI server accepts a PDB file containing ANISOU records or TLS records.

Eric Martz: /* Some records that include ANISOU records */

Eric Martz — Sat, 23 Apr 2011 00:55:44 GMT

Some records that include ANISOU records

←Older revision		Revision as of 00:55, 23 April 2011
Line 18:		Line 18:
	* The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic [[Temperature value#Data Format\|temperature factors]] as B(eq), as described in the ATOM and HETATM sections.		* The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic [[Temperature value#Data Format\|temperature factors]] as B(eq), as described in the ATOM and HETATM sections.

-	==Some ~~records~~ that include ANISOU records==	+	==Some PDB entries that include ANISOU records==
	* [[3kg2]]		* [[3kg2]]

Eric Martz: /* See Also */

Eric Martz — Sat, 23 Apr 2011 00:55:25 GMT

Wayne Decatur at 03:37, 10 July 2010

Wayne Decatur — Sat, 10 Jul 2010 03:37:07 GMT

←Older revision		Revision as of 03:37, 10 July 2010
Line 19:		Line 19:

	==Some records that include ANISOU records==		==Some records that include ANISOU records==
-	[[3kg2]]	+	* [[3kg2]]

	==Related==		==Related==
Line 26:		Line 26:
	==See Also==		==See Also==
	[[Temperature value]]		[[Temperature value]]
		+	[[Quality assessment for molecular models]]

	==References==		==References==
	<ref group="xtra">PMID: 10329772</ref><references group="xtra"/><ref group="xtra">PMID: 10666575</ref><references group="xtra"/><ref group="xtra">PMID: 15809496</ref><references group="xtra"/>		<ref group="xtra">PMID: 10329772</ref><references group="xtra"/><ref group="xtra">PMID: 10666575</ref><references group="xtra"/><ref group="xtra">PMID: 15809496</ref><references group="xtra"/>

Wayne Decatur at 03:33, 10 July 2010

Wayne Decatur — Sat, 10 Jul 2010 03:33:55 GMT

←Older revision		Revision as of 03:33, 10 July 2010
Line 16:		Line 16:
	* ANISOU values are listed only if they have been provided by the depositor. The depositor provides ANISOU records, PDB verifies their format.		* ANISOU values are listed only if they have been provided by the depositor. The depositor provides ANISOU records, PDB verifies their format.

-	* The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic temperature factors as B(eq), as described in the ATOM and HETATM sections.	+	* The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic [[Temperature value#Data Format\|temperature factors]] as B(eq), as described in the ATOM and HETATM sections.

	==Some records that include ANISOU records==		==Some records that include ANISOU records==
	[[3kg2]]		[[3kg2]]

		+	==Related==
		+	[http://pymmlib.sourceforge.net/doc/tlsview/tlsview.html TLSView]: A Molecular Viewer for TLS Rigid Body Motion
		+
		+	==See Also==
		+	[[Temperature value]]

	==References==		==References==
	<ref group="xtra">PMID: 10329772</ref><references group="xtra"/><ref group="xtra">PMID: 10666575</ref><references group="xtra"/><ref group="xtra">PMID: 15809496</ref><references group="xtra"/>		<ref group="xtra">PMID: 10329772</ref><references group="xtra"/><ref group="xtra">PMID: 10666575</ref><references group="xtra"/><ref group="xtra">PMID: 15809496</ref><references group="xtra"/>

Wayne Decatur: /* Analysis */

Wayne Decatur — Sat, 10 Jul 2010 03:30:38 GMT

Analysis

←Older revision		Revision as of 03:30, 10 July 2010
Line 3:		Line 3:
	==Analysis==		==Analysis==
	[http://skuld.bmsc.washington.edu/parvati/parvati.html PARVATI] - Protein Anisotropic Refinement Validation and Analysis Tool.		[http://skuld.bmsc.washington.edu/parvati/parvati.html PARVATI] - Protein Anisotropic Refinement Validation and Analysis Tool.
-	~~[http://pymmlib~~.~~sourceforge.net/doc/tlsview/tlsview.html TLSView]: A Molecular Viewer for TLS Rigid Body Motion~~	+	The PARVATI server accepts a PDB file containing ANISOU records or TLS records.
		+

	The PARVATI server accepts a PDB file containing ANISOU records or TLS records.		The PARVATI server accepts a PDB file containing ANISOU records or TLS records.

Wayne Decatur at 03:29, 10 July 2010

Wayne Decatur — Sat, 10 Jul 2010 03:29:03 GMT

←Older revision		Revision as of 03:29, 10 July 2010
Line 16:		Line 16:

	* The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic temperature factors as B(eq), as described in the ATOM and HETATM sections.		* The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic temperature factors as B(eq), as described in the ATOM and HETATM sections.
		+
		+	==Some records that include ANISOU records==
		+	[[3kg2]]
		+

	==References==		==References==
	<ref group="xtra">PMID: 10329772</ref><references group="xtra"/><ref group="xtra">PMID: 10666575</ref><references group="xtra"/><ref group="xtra">PMID: 15809496</ref><references group="xtra"/>		<ref group="xtra">PMID: 10329772</ref><references group="xtra"/><ref group="xtra">PMID: 10666575</ref><references group="xtra"/><ref group="xtra">PMID: 15809496</ref><references group="xtra"/>

Wayne Decatur at 03:26, 10 July 2010

Wayne Decatur — Sat, 10 Jul 2010 03:26:18 GMT

←Older revision		Revision as of 03:26, 10 July 2010
Line 18:		Line 18:

	==References==		==References==
-	<ref group="xtra">PMID: 10329772</ref><ref group="xtra">PMID: 10666575</ref><ref group="xtra">PMID:15809496/ref><references group="xtra"/>	+	<ref group="xtra">PMID: 10329772</ref><references group="xtra"/><ref group="xtra">PMID: 10666575</ref><references group="xtra"/><ref group="xtra">PMID: 15809496</ref><references group="xtra"/>
-	~~{{Reflist}}~~	+

Wayne Decatur: started page

Wayne Decatur — Sat, 10 Jul 2010 03:23:14 GMT

started page

New page

Anisotropic refinement is included among the [http://www.msg.ucsf.edu/local/programs/shelxl/ch_08.html strategies for macromolecular refinement].

==Analysis==
[http://skuld.bmsc.washington.edu/parvati/parvati.html PARVATI] - Protein Anisotropic Refinement Validation and Analysis Tool.
[http://pymmlib.sourceforge.net/doc/tlsview/tlsview.html TLSView]: A Molecular Viewer for TLS Rigid Body Motion

The PARVATI server accepts a PDB file containing ANISOU records or TLS records.

==ANISOU records==
* The ANISOU records present the anisotropic temperature factors.
* The anisotropic temperature factors (columns 29 - 70) are scaled by a factor of 10**4 (Angstroms**2) and are presented as integers.

* The anisotropic temperature factors are stored in the same coordinate frame as the atomic coordinate records.

* ANISOU values are listed only if they have been provided by the depositor. The depositor provides ANISOU records, PDB verifies their format.

* The anisotropic temperature factors are related to the corresponding ATOM/HETATM isotropic temperature factors as B(eq), as described in the ATOM and HETATM sections.

==References==
<ref group="xtra">PMID: 10329772</ref><ref group="xtra">PMID: 10666575</ref><ref group="xtra">PMID:15809496/ref><references group="xtra"/>
{{Reflist}}

←Older revision		Revision as of 00:55, 23 April 2011
Line 25:		Line 25:

	==See Also==		==See Also==
-	[[Temperature value]]	+	*[[Temperature value]]
-	[[Quality assessment for molecular models]]	+	*[[Quality assessment for molecular models]]

	==References==		==References==
	<ref group="xtra">PMID: 10329772</ref><references group="xtra"/><ref group="xtra">PMID: 10666575</ref><references group="xtra"/><ref group="xtra">PMID: 15809496</ref><references group="xtra"/>		<ref group="xtra">PMID: 10329772</ref><references group="xtra"/><ref group="xtra">PMID: 10666575</ref><references group="xtra"/><ref group="xtra">PMID: 15809496</ref><references group="xtra"/>