Anisotropic refinement
From Proteopedia
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==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. | ||
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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. | ||
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* 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 | + | ==Some PDB entries that include ANISOU records== |
| - | [[3kg2]] | + | * [[3kg2]] |
| + | * [[4un3]], [[4un4]], and [[4un5]] | ||
==Related== | ==Related== | ||
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==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"/> | ||
Current revision
Anisotropic refinement is included among the strategies for macromolecular refinement.
Contents |
Analysis
PARVATI - Protein Anisotropic Refinement Validation and Analysis Tool. 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.
Some PDB entries that include ANISOU records
Related
TLSView: A Molecular Viewer for TLS Rigid Body Motion
See Also
References
- Merritt EA. Expanding the model: anisotropic displacement parameters in protein structure refinement. Acta Crystallogr D Biol Crystallogr. 1999 Jun;55(Pt 6):1109-17. PMID:10329772
- Merritt EA. Comparing anisotropic displacement parameters in protein structures. Acta Crystallogr D Biol Crystallogr. 1999 Dec;55(Pt 12):1997-2004. PMID:10666575
- Painter J, Merritt EA. A molecular viewer for the analysis of TLS rigid-body motion in macromolecules. Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):465-71. Epub 2005, Mar 24. PMID:15809496 doi:10.1107/S0907444905001897
