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Hello Mike, I would recommend PyMOL. Consider this example: # get structures from PDB fetch 2j0s, async=0 fetch 2j0u, async=0 # remove alternative configurations remove not alt +A # select conformers with c-alpha atoms select conf1, 2j0s and chain A and name CA select conf2, 2j0u and chain A and name CA # select domains select dom1, resi 69-239 select dom2, resi 250-411 # superimpose on dom1 and calculate RMSD for dom2 fit (conf1 like conf2) and dom1, (conf2 like conf1) and dom1 rms_cur (conf1 like conf2) and dom2, (conf2 like conf1) and dom2 Cheers, Thomas On Wed, 2010-12-29 at 13:52 +0000, Michael Swan wrote: > Dear all, > I am having a bit of trouble finding a program to do an rmsd > calculation and give me the differences between all the atoms in the > structures. > I have two structures which are identical in the sense that one is the > apo protein and one is the bound structure. I would like to > superimpose them using only one domain then output the rmsd values for > all the atoms or at least individual residues. The structures are not > completely identical as some extra residues were visible in the bound > structure so I hope there is a program that can ignore those > differences. > If anyone knows of a program that will do this calculation I would > much appreciate hearing about it. There seem to be many programs that > will give an average rmsd over the whole structure or just the region > used for alignment but I haven't found anything that will give me > distances between atoms or residues that were not used in the > alignment. > Thanks, > Mike. -- Thomas Holder AG Jekely MPI for Developmental Biology Spemannstr. 35 D-72076 Tuebingen