Hi Smita Yes, that’s the kind of analysis I had in mind.
I have > 700 structures to “look” at so something that would say “these residues overlay with a small RMSD so this bit is rigid, but these residues don’t, so that part is flexible” ~700 times. Using an MG program of any kind would just be a sanity check that I’d use on a very few structures (probably no more than ~20-30) to make sure I’m happy with the results before automating the whole thing. Harry > On 26 May 2021, at 16:29, S. Mohanty <bionm...@yahoo.com> wrote: > > Hi Harry, > > The superpose/overlay of all the structures in PyMol should inform you the > rigid part of the protein as well as the flexible part. The rigid part would > have very low backbone RMSD or overlay tightly and the flexible part (loops, > N-term and C-term etc.) would not superpose tightly. If you check literature, > the dynamics of the protein may have been studied through NMR relaxation. > > Smita > > > On Wednesday, May 26, 2021, 10:05:05 AM CDT, Harry Powell - CCP4BB > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > > Hi > > Given that there are plenty of people on this BB who are structural > biologists rather than “just” crystallographers, I thought someone here might > be able to help. > > If I have a structure in the PDB (e.g. 2kv5) that is an ensemble of > structures that fit the NOEs, is there a tool available that will give me > some idea about the bits of the structure that do not vary much (“rigid”) and > the bits that are all over the place (“flexible”)? > > Would superpose or gesamt be a good tool for this? Ideally I’d like something > that could add a figure to the B columns in a PDB file so I could see > something in QTMG (or PyMol if forced…) or do other useful things with the > information. > > Harry > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
