Hi Oarabile, Coot allows you to align structures by selected atoms: https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/docs/coot-faq.html#How-do-I-do-a-superposition-on-just-a-part-of-my-structure_003f I guess what you are trying to do can be accomplished by the “multi-range LSQ superposition” method.
Note that the commands shown in the above page are in Guile/Scheme format, which is now not supported in Coot (if I am correct). You need to write the commands in python format like this: superpose_with_atom_selection (0, "//B/1-100”, 1, "//B/1-100",0) -basically: i)replace all ‘-’with ‘_’in function name, ii) put all parameters in a pair of brackets and iii) separate them with commas. For python formatting see https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Python You can either make a little txt file “scripts.py” with these commands and let Coot run it, or you can type them one by one in Calculate-Scripting-python. Zhijie From: Kgosisejo, Oarabile Sent: Thursday, February 05, 2015 5:41 PM To: [email protected] Subject: [ccp4bb] Superposition of select residues Hi all, Does anyone know of a program to use to superpose only selected protein residues, e.g. enzyme active site residues. I solved my structure using molecular replacement now I want to compare its active site to those of homologous structures. I have used the DALI server before but I had to upload the whole model. Thank you for your advise Best Regards, Oarabile M. Kgosisejo, MSc. Candidate University of Saskatchewan [email protected]
