Structure superposition tools: Difference between revisions
Eric Martz (talk | contribs) |
some details abot FATCAT output |
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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). | ||
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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=== | ||
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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 | **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. | ||
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==Structural Superposition Software== | ==Structural Superposition Software== | ||
This section is for stand-alone software packages that do not require a web browser. | This section is for stand-alone software packages that do not require a web browser. | ||
===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. | *Version 4.11 released in 2019; works on Windows and macOS 10.5-10.14. | ||
*'''Caution''': This program | *'''Caution''': This program may report the wrong number of alpha carbons superposed, typically reporting twice or four-times the actual number. In order to get the correct count, use the Fit menu, Calculate RMS, or observe the number of residues selected in each layer. | ||
*Help: YES. | *Help: YES. | ||
* Fit, Magic Fit does a '''sequence-based''' structural | * Fit, Magic Fit does a '''sequence-based''' structural superposition. | ||
* Fit, Iterative Magic Fit starts with a sequence-based structural | * Fit, Iterative Magic Fit starts with a sequence-based structural superposition, then does further structural superposition over a smaller number of residues, further minimizing the RMSD. | ||
* Fit, Explore Domain Alternate Fits: does a '''sequence-independent''' structural | * Fit, Explore Domain Alternate Fits: does a '''sequence-independent''' structural superposition. | ||
* Magic Fit and Iterative Magic Fit can '''align multiple chains in each model''' and can '''align DNA chains''' as well as protein chains. | * Magic Fit and Iterative Magic Fit can '''align multiple chains in each model''' and can '''align DNA chains''' as well as protein chains. | ||
* Color, RMS: colors the target structure by deviation. | * Color, RMS: colors the target structure by deviation. | ||
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===Jmol=== | ===Jmol=== | ||
See | |||
* [[Superposition | * [[Jmol/Superposition]] which explains the method in Jmol. | ||
* [[Samatey/1#Comparison]] which shows an animation of alignment performed by Jmol. | * [[Samatey/1#Comparison]] which shows an animation of alignment performed by Jmol. | ||
* [[Samatey/2#Comparison_with_Thermotoga]] which has buttons that animate the alignments of different domains. | * [[Samatey/2#Comparison_with_Thermotoga]] which has buttons that animate the alignments of different domains. | ||
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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 | *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]. | ||
===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 | *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=== | ||
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===Example Requiring Flexibility=== | ===Example Requiring Flexibility=== | ||
'''This example requires flexibility for a good | 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. | ||
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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 | 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 | 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"(?) | ||
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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 | *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 | *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 | *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 | *3.2 Å RMSD RIGID superposition included 299 residues. | ||
*Z-score: 25.5. | *Z-score: 25.5. | ||
*13% sequence identity for the structurally | *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 | **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 | **1.69 Å RMSD for 159 superposed residues. | ||
*Explore Domain Alternate Fits -- sequence-independent | *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 | **1.0 Å for 64 superposed residues. | ||
====FATCAT example==== | ====FATCAT example==== | ||
*3.02 Å RMSD RIGID | *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 | *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 | *FLEXIBLE superposition introduced ZERO twists (hinges), so gave the same result as the rigid superposition. | ||
====MAMMOTH example==== | ====MAMMOTH example==== | ||
*4.0 Å (?) with 298 | *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 | **4.5 Å RMSD for 197 superposed residues. | ||
====TM-Align example==== | ====TM-Align example==== | ||
*3.42 Å for 312 | *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. | *2.9 Å RMSD. Superposition includes 275 residues. | ||
*13% sequence identity in the | *13% sequence identity in the superposed regions. | ||
*Tried the example requiring flexibility (above) as a second case. A 52 residue subdomain was | *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 | * 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 | * 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 /> | ||