Structure superposition tools - Revision history

Angel Herraez: some details abot FATCAT output

2024-04-03T14:22:49Z

some details abot FATCAT output

← Older revision		Revision as of 14:22, 3 April 2024
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	*Visualization: YES.		*Visualization: YES.
	*Color by deviation: '''NO'''. (Colors identify twist/hinge boundaries.)		*Color by deviation: '''NO'''. (Colors identify twist/hinge boundaries.)
	*Offered by RCSB? YES		*Offered by RCSB? YES, with both options: rigid and flexible.
			*Download result: one pdb file, not using MODEL/ENDMDL delimiters but with the aligned structures labeled as chains A and B. If done at RCSB, download has 2 separate mmCIF files.
	*Special features:		*Special features:
	**Produces a [[morph]] between the two superposed chains (at the link "Interpolating between ...").		**Produces a [[morph]] between the two superposed chains (at the link "Interpolating between ..."). It is a 10-model PDB file '''with only alpha carbons'''.
	**Offers a RasMol script to color each rigid segment distinctly (separated by twists/hinges).		**Offers a RasMol script to color each rigid segment distinctly (separated by twists/hinges).

Eric Martz: /* DeepView = Swiss-PDBViewer */

2023-09-28T21:49:11Z

DeepView = Swiss-PDBViewer

← Older revision		Revision as of 21:49, 28 September 2023
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	===DeepView = Swiss-PDBViewer===		===DeepView = Swiss-PDBViewer===
	*Download site: [http://www.expasy.org/spdbv/ DeepView Swiss-PdbViewer].		*Download site: [http://www.expasy.org/spdbv/ DeepView Swiss-PdbViewer].
			*[https://spdbv.unil.ch/superpos_tut.html Tutorial on superposition using DeepView].
	*Publications (1997, 1999)<ref>PMID: 9504803</ref><ref>PMID: 10470037</ref>		*Publications (1997, 1999)<ref>PMID: 9504803</ref><ref>PMID: 10470037</ref>
	*Version 4.11 released in 2019; works on Windows and macOS 10.5-10.14.		*Version 4.11 released in 2019; works on Windows and macOS 10.5-10.14.

Eric Martz: /* SuperPose */

2023-09-28T21:47:46Z

SuperPose

← Older revision		Revision as of 21:47, 28 September 2023
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	*Search with uploaded models: YES		*Search with uploaded models: YES
	*Color by deviation: ?		*Color by deviation: ?
	*Special features: ?		*Special features:
			** Allows specification of restricted regions to superpose.

	===TM-Align===		===TM-Align===

Markus Wiederstein: added publication on TopMatch-web (2020)

2023-09-11T08:36:07Z

added publication on TopMatch-web (2020)

← Older revision		Revision as of 08:36, 11 September 2023
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	*Server: [http://topmatch.services.came.sbg.ac.at/ TopMatch]		*Server: [http://topmatch.services.came.sbg.ac.at/ TopMatch]
	*Publications (both 2008)<ref name="topmatch">PMID: 18174182</ref><ref name="topmatch2">PMID: 18227113</ref>, (2012)<ref name="topmatch3">PMID: 22483118</ref>		*Publications (both 2008)<ref name="topmatch">PMID: 18174182</ref><ref name="topmatch2">PMID: 18227113</ref>, (2012)<ref name="topmatch3">PMID: 22483118</ref>, (2020)<ref name="topmatch4">PMID: 32479639</ref>
	*Help on server: YES.		*Help on server: YES.
	*Does superposition involve sequence comparison? NO.		*Does superposition involve sequence comparison? NO.
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	*Multiple superposition: NO.		*Multiple superposition: NO.
	*Structure-based sequence alignment: YES.		*Structure-based sequence alignment: YES.
	*Structure neighbors (pre-calculated): NO (but see TopSearch).		*Structure neighbors (pre-calculated): NO (but see [[#TopSearch\|TopSearch]]).
	*Pairwise superposition including uploaded models: YES		*Pairwise superposition including uploaded models: YES
	*Visualization: YES.		*Visualization: YES.
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	*Offered by RCSB? NO.		*Offered by RCSB? NO.
	*Special features:		*Special features:
	**Structure superposition of ~~multiprotein~~ complexes.		**Structure superposition of multichain complexes (of both proteins and nucleic acids).
	**You can download the superposition target PDB file (in a separate file from the query PDB file). A PyMOL script is also available, as is the matrix to transform the target coordinates.		**You can download the superposition target PDB file (in a separate file from the query PDB file). A PyMOL script is also available, as is the matrix to transform the target coordinates.

Eric Martz: /* Examples for Rigid Alignment */

2021-09-20T23:51:54Z

Examples for Rigid Alignment

← Older revision		Revision as of 23:51, 20 September 2021
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	Example 1<br>Summary for 1fszA vs. 1tubA		Example 1<br>Summary for 1fszA vs. 1tubA
	</td></tr><tr><td>		</td></tr><tr><td>
	Tool</td><td>Residues ~~Aligned~~</td><td>RMSD, Å</td><td>~~Unaligned~~ Residues /Total		Tool</td><td>Residues Superposed</td><td>RMSD, Å</td><td>Residues Not Superposed/Total
	</td></tr><tr><td>		</td></tr><tr><td>
	CE</td><td>305</td><td>3.2</td><td>96/401		CE</td><td>305</td><td>3.2</td><td>96/401
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	Example 2<br>Mammalian tubulin α vs. β, 1tubA (length 440) vs. 1tubB (length 427): 40% sequence identity.		Example 2<br>Mammalian tubulin α vs. β, 1tubA (length 440) vs. 1tubB (length 427): 40% sequence identity.
	</td></tr><tr><td>		</td></tr><tr><td>
	Tool</td><td>Residues ~~Aligned~~</td><td>RMSD, Å</td><td>~~Unaligned~~ Residues		Tool</td><td>Residues Superposed</td><td>RMSD, Å</td><td>Residues Not Superposed
	</td></tr><tr><td>		</td></tr><tr><td>
	CE</td><td>404</td><td>1.34</td><td>56/"460"(?)		CE</td><td>404</td><td>1.34</td><td>56/"460"(?)

Eric Martz: /* Examples for Rigid Alignment */

2021-09-20T23:50:01Z

Examples for Rigid Alignment

← Older revision		Revision as of 23:50, 20 September 2021
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	<tr><td>Topmatch</td><td>416</td><td>1.68		<tr><td>Topmatch</td><td>416</td><td>1.68
	</td></tr></table>		</td></tr></table>
	[[1fsz]] is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin<ref>PMID: 9628483</ref><ref>PMID: 20459678</ref> found in [[1tub]] chain A, length 440. However, the sequence identity is low. 92/372 residues can be aligned with 19% identity (2 gaps), and another 14 residue stretch with 42% identity (no gaps).		[[1fsz]] is the bacterial cell division protein FtsZ, length 334 residues with coordinates (372 in crystallized protein). It has structural similarity to mammalian tubulin<ref>PMID: 9628483</ref><ref>PMID: 20459678</ref> found in [[1tub]] chain A, length 440. However, the sequence identity is low. 92/372 residues can be aligned with 19% identity (2 gaps), and another 14 residue stretch with 42% identity (no gaps). '''Tests in this section were performed in 2011.'''
	====CE example====		====CE example====
	*3.2 Å RMSD for 305 residues. The structural ~~alignment~~ has 96 unaligned "gap" residues: one large gap of ~30 residues, and ten smaller gaps of 8 residues or less.		*3.2 Å RMSD for 305 residues. The structural superposition has 96 unaligned "gap" residues: one large gap of ~30 residues, and ten smaller gaps of 8 residues or less.
	*Z-score: 6.5.		*Z-score: 6.5.
	*12.5% sequence identity within the structural ~~alignment~~.		*12.5% sequence identity within the structural superposition.
	*Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software ~~(see above)~~.		*Same results obtained at either the CE website, or using the ''Calculate Structure Alignment'' java webstart software.

	====Dali example====		====Dali example====
	*3.2 Å RMSD RIGID ~~alignment~~ included 299 residues.		*3.2 Å RMSD RIGID superposition included 299 residues.
	*Z-score: 25.5.		*Z-score: 25.5.
	*13% sequence identity for the structurally ~~aligned~~ regions.		*13% sequence identity for the structurally superposed regions.
	*The structure-based sequence alignment has many gaps.		*The structure-based sequence alignment has many gaps.

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	Tested with version 4.01 OS X.		Tested with version 4.01 OS X.
	*Magic Fit -- SEQUENCED-BASED:		*Magic Fit -- SEQUENCED-BASED:
	**4.4 Å RMSD for 114 ~~aligned~~ residues.		**4.4 Å RMSD for 114 superposed residues.
	*Iterative Magic Fit -- Sequence based followed by RMSD minimization:		*Iterative Magic Fit -- Sequence based followed by RMSD minimization:
	**1.69 Å RMSD for 159 ~~aligned~~ residues.		**1.69 Å RMSD for 159 superposed residues.
	*Explore Domain Alternate Fits -- sequence-independent ~~alignment~~:		*Explore Domain Alternate Fits -- sequence-independent superposition:
	**Used option NOT to use selected residues.		**Used option NOT to use selected residues.
	**Nevertheless program complained repeatedly that I had not selected residues.		**Nevertheless program complained repeatedly that I had not selected residues.
	**Nevertheless program produced an alignment:		**Nevertheless program produced an alignment:
	**1.0 Å for 64 ~~aligned~~ residues.		**1.0 Å for 64 superposed residues.

	====FATCAT example====		====FATCAT example====
	*3.02 Å RMSD RIGID ~~alignment~~ includes 298 residues.		*3.02 Å RMSD RIGID superposition includes 298 residues.
	*P value: 5 x 10<sup>-8</sup> (used instead of z-score to take twists into account).		*P value: 5 x 10<sup>-8</sup> (used instead of z-score to take twists into account).
	*10.2% sequence identity in the structurally ~~aligned~~ regions.		*10.2% sequence identity in the structurally superposed regions.
	*The structure-based sequence alignment has many gaps, looking similar to that generated by CE.		*The structure-based sequence alignment has many gaps, looking similar to that generated by CE.
	*FLEXIBLE ~~alignment~~ introduced ZERO twists (hinges), so gave the same result as the rigid ~~alignment~~.		*FLEXIBLE superposition introduced ZERO twists (hinges), so gave the same result as the rigid superposition.

	====MAMMOTH example====		====MAMMOTH example====
	*4.0 Å (?) with 298 ~~aligned~~ residues (?) (Labeling in results is unclear.)		*4.0 Å (?) with 298 superposed residues (?) (Labeling in results is unclear.)
	*Structure-based sequence alignment is displayed.		*Structure-based sequence alignment is displayed.

	====PyMOL example====		====PyMOL example====
	*Command: super 1fsz////CA, 1tub_a////CA, object=supAB		*Command: super 1fsz////CA, 1tub_a////CA, object=supAB
	**4.5 Å RMSD for 197 ~~aligned~~ residues.		**4.5 Å RMSD for 197 superposed residues.

	====TM-Align example====		====TM-Align example====
	*3.42 Å for 312 ~~aligned~~ residues.		*3.42 Å for 312 superposed residues.
	*Structure-based sequence alignment is displayed.		*Structure-based sequence alignment is displayed.

	====TopMatch example====		====TopMatch example====
	*2.9 Å RMSD. ~~Alignment~~ includes 275 residues.		*2.9 Å RMSD. Superposition includes 275 residues.
	*13% sequence identity in the ~~aligned~~ regions.		*13% sequence identity in the superposed regions.
	*Tried the example requiring flexibility (above) as a second case. A 52 residue subdomain was ~~aligned~~ with RMSD 2.69 Å, an alternative ~~alignment~~ matching the second domain shows up with 47 residues/RMSD 2.69 Å.		*Tried the example requiring flexibility (above) as a second case. A 52 residue subdomain was superposed with RMSD 2.69 Å, an alternative superposition matching the second domain shows up with 47 residues/RMSD 2.69 Å.

	====VAST example====		====VAST example====
	* 4.0 Å RMSD for 299 ~~aligned~~ residues.		* 4.0 Å RMSD for 299 superposed residues.
	* Expectation value: 10<sup>-16</sup>.		* Expectation value: 10<sup>-16</sup>.
	* 11.4% sequence identity in the ~~aligned~~ segments.		* 11.4% sequence identity in the superposed segments.
	* '''I could find no way to download the aligned PDB file for visualization in Jmol or RasMol.'''		* '''I could find no way to download the aligned PDB file for visualization in Jmol or RasMol.'''

	==References==		==References==
	<references />		<references />

Eric Martz: /* Example Requiring Flexibility */

2021-09-20T23:42:35Z

Example Requiring Flexibility

← Older revision		Revision as of 23:42, 20 September 2021
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	===Example Requiring Flexibility===		===Example Requiring Flexibility===

	'''This example requires flexibility for a good superposition''': [[2bbm]]:A vs. [[1cfc]]:A. Length: 148. 97% sequence identity (145/148), 99% similar. These files contain calmodulin. In [[2bbm]] (''Drosophila''), the two calcium-binding domains are wrapped around a peptide. In [[1cfc]] (''Xenopus''), there is no calcium and no peptide, and the linker between the two domains is flexible.		Tests performed in 2011. '''This example requires flexibility for a good superposition''': [[2bbm]]:A vs. [[1cfc]]:A. Length: 148. 97% sequence identity (145/148), 99% similar. These files contain calmodulin. In [[2bbm]] (''Drosophila''), the two calcium-binding domains are wrapped around a peptide. In [[1cfc]] (''Xenopus''), there is no calcium and no peptide, and the linker between the two domains is flexible.
	*CE:		*CE:
	**4.8 Å RMSD.		**4.8 Å RMSD.

Eric Martz: /* Example Requiring Flexibility */

2021-09-20T23:41:02Z

Example Requiring Flexibility

← Older revision		Revision as of 23:41, 20 September 2021
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	===Example Requiring Flexibility===		===Example Requiring Flexibility===

	'''This example requires flexibility for a good ~~alignment~~''': [[2bbm]]:A vs. [[1cfc]]:A. Length: 148. 97% sequence identity (145/148), 99% similar. These files contain calmodulin. In [[2bbm]] (''Drosophila''), the two calcium-binding domains are wrapped around a peptide. In [[1cfc]] (''Xenopus''), there is no calcium and no peptide, and the linker between the two domains is flexible.		'''This example requires flexibility for a good superposition''': [[2bbm]]:A vs. [[1cfc]]:A. Length: 148. 97% sequence identity (145/148), 99% similar. These files contain calmodulin. In [[2bbm]] (''Drosophila''), the two calcium-binding domains are wrapped around a peptide. In [[1cfc]] (''Xenopus''), there is no calcium and no peptide, and the linker between the two domains is flexible.
	*CE:		*CE:
	**4.8 Å RMSD.		**4.8 Å RMSD.

Eric Martz: /* UCSF Chimera */

2021-09-20T23:38:26Z

UCSF Chimera

← Older revision		Revision as of 23:38, 20 September 2021
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	===UCSF Chimera===		===UCSF Chimera===
	*Download site: [https://www.cgl.ucsf.edu/chimera/download.html]		*Download site: [https://www.cgl.ucsf.edu/chimera/download.html www.cgl.ucsf.edu/chimera/download.html]
	*The ''matchmaker'' command does structural ~~alignment~~, see [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html here]. Or use "match" to specify exact atom pairs, see [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html here]		*The ''matchmaker'' command does structural superposition, see [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html here]. Or use "match" to specify exact atom pairs, see [https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/superposition.html here]
	*Color by RMSD: YES [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012379.html steps outlined under '(4)'] or [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-April/007393.html Under '(A)' here]		*Color by RMSD: YES [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2016-June/012379.html steps outlined under '(4)'] or [http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-April/007393.html Under '(A)' here]


	===TopMatch===		===TopMatch===

Eric Martz: /* PyMOL */

2021-09-20T23:36:37Z

PyMOL

← Older revision		Revision as of 23:36, 20 September 2021
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	===PyMOL===		===PyMOL===
	*Download site: [http://www.pymol.org/ PyMOL.Org]		*Download site: [http://www.pymol.org/ PyMOL.Org]
	*The ''super'' command does structural ~~alignment~~.		*The ''super'' command does structural superposition.
	*Color by RMSD: YES [http://www.pymolwiki.org/index.php/ColorByRMSD example].		*Color by RMSD: YES [http://www.pymolwiki.org/index.php/ColorByRMSD example].