id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4690 Simplify computing CA RMSD of an ensemble of structures. Tom Goddard Eric Pettersen "Current steps for computing the CA RMSD of a set of structures are complex https://www.cgl.ucsf.edu/pipermail/chimera-users/2014-March/009709.html and the question of how to do it has been raised many times on the Chimera and ChimeraX user lists. We should have a trivial command or gui way to do this commonly needed task. Should also set an attribute to allow easy coloring by CA RMSD. Tristan addressed this in his answer to a CCP4 mailing list question: On May 26, 2021, at 10:29 AM, Tristan Croll wrote: Thought you might be interested. Just sent him a quick-and-dirty ChimeraX script to color by CA-RMS (attached as .txt since Outlook gets grumpy with me otherwise)... but seems like it might be a neat little addition? Would use the bug report system but the server's down. From: CCP4 bulletin board on behalf of Harry Powell - CCP4BB <0000193323b1e616-dmarc-request@JISCMAIL.AC.UK> Sent: 26 May 2021 16:04 To: 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" defect accepted moderate Structure Analysis Elaine Meng Tristan Croll all ChimeraX