Structural superposition: Difference between revisions
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# | # [http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/matchmaker/matchmaker.html MatchMaker] which is part of [http://www.cgl.ucsf.edu/chimera Chimera] | ||
# O | # [http://xray.bmc.uu.se/alwyn/A-Z_of_O/A-Z_frameset.html O] | ||
# lsqman | # [http://xray.bmc.uu.se/usf/lsqman_man.html lsqman] | ||
# lsqkab | # [http://www.ccp4.ac.uk/html/lsqkab.html lsqkab] | ||
# coot | # [[coot]] | ||
# | # [http://www.theseus3d.org/ Theseus] is a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood. | ||
# | # [http://webapps.embl-hamburg.de/escet/ Escet] good for finding subtle differences, or the common core | ||
# Using CCP4i: go to the coordinate utility - Superpose molecules - You can either compare things using secondary structure or by specifying residue spans. Underlying programs are PISA (also available at the BI msd server) and LSQKAB | |||
# CCP4: superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ] Only bear in mind that [http://www.ccp4.ac.uk/html/superpose.html superpose] relies on the presence of secondary structure, so that your selections should always include at least 3 SSEs. | |||
# MUSTANG - http://pxgrid.med.monash.edu.au:8080/mustangserver/ | |||
# FATCAT - [http://fatcat.burnham.org/fatcat-cgi/cgi/fatcat.pl?-func=pairwise flexible alignment] | |||
# or just choose one of the 84 or so entries in [http://en.wikipedia.org/wiki/Structural_alignment_software Wikipedia] | |||
Latest revision as of 17:41, 29 May 2011
- MatchMaker which is part of Chimera
- O
- lsqman
- lsqkab
- coot
- Theseus is a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood.
- Escet good for finding subtle differences, or the common core
- Using CCP4i: go to the coordinate utility - Superpose molecules - You can either compare things using secondary structure or by specifying residue spans. Underlying programs are PISA (also available at the BI msd server) and LSQKAB
- CCP4: superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ] Only bear in mind that superpose relies on the presence of secondary structure, so that your selections should always include at least 3 SSEs.
- MUSTANG - http://pxgrid.med.monash.edu.au:8080/mustangserver/
- FATCAT - flexible alignment
- or just choose one of the 84 or so entries in Wikipedia