https://pubmed.ncbi.nlm.nih.gov/8744573/
Old but worked... Best br On Wed, May 26, 2021, 19:43 Tristan Croll <ti...@cam.ac.uk> wrote: > (sending properly this time, rather than just to Rasmus) > > I don't believe a "color by RMS" option is in ChimeraX right now (I'll > suggest it to the developers), but this will align all models then set > B-factors for each residue to the RMS CA deviation from the mean position. > Could be extended fairly trivially to do all-atom RMS if you wanted to. > Change the extension for the attached text file to .py, open your NMR > ensemble in ChimeraX, select all the models (typically just "sel #1" should > do the trick), then use File/Open and choose color_by_rms.py (or just "open > color_by_rms.py" on the command line if it's in your working directory). As > long as all models have the same set of residues, it should do the trick. > Example image for 2kv5 attached. > > Have fun! > > -- Tristan > ------------------------------ > *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Harry > Powell - CCP4BB <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> > *Sent:* 26 May 2021 16:04 > *To:* CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > *Subject:* [ccp4bb] Analysis of NMR ensembles > > 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 > ######################################################################## 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/
