Structural superposition

From CCP4 wiki
(Redirected from Superimposing Molecules)
  1. MatchMaker which is part of Chimera
  2. O
  3. lsqman
  4. lsqkab
  5. coot
  6. 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.
  7. Escet good for finding subtle differences, or the common core
  8. 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
  9. 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.
  10. MUSTANG - http://pxgrid.med.monash.edu.au:8080/mustangserver/
  11. FATCAT - flexible alignment
  12. or just choose one of the 84 or so entries in Wikipedia