Structure superposition tools: Difference between revisions
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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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===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. | ||
