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chimerax-users@cgl.ucsf.edu

December 2024

33 participants
42 discussions

Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change.
by Elaine Meng 02 Dec '24

02 Dec '24

Hi Evan, Your image looks nice! From your screenshot I can see you are using ChimeraX (not Chimera) so I will answer for ChimeraX ( there is a different email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here). To "play" the conformational change there are a couple of options: (1) if the models are already open as a set of multiple models as shown in your screenshot, you can use command: mseries slider #1 ...which will open a slider interface that you can click play, record movie, etc. Or, you can play through the series with the "mseries" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mseries.html> (2) Or, you can use the "coordsets true" option of the "open" command when opening the file, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#coordsets> which means to interpret the file as a single trajectory instead of a series of models. That will automatically show a slider interface. Example: open blahblah.pdb coordset true If you want to use the file browser to find your PDB file, you can use command open browse coordsets true ...and it will open the file browser for you to find and choose the file. If you have a trajectory, you can also play through it with the separate "coordset" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> More info, general explanation of model series vs. trajectories <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 2, 2024, at 1:31 PM, Evan Kantrowitz via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > Can someone give me help with a, I think, simple issue. I have a single pdb file containing 30 MODELS > These 30 models correspond to a conformational change. Here is a portion of the Models list > > When I read it in,I see all 30 models showing in the view. > What I want to do is make a movie showing these 30 MODELS one after the other. I have tried coordset and coordset slider but have not got it to work. > > Thanks > > Evan > > PS. This is what the image looks like with the 30 frames.It was generated from the A chain of pdb files 2e2n and 2e2q using the website ViewMotions (viewmotions.bc.edu) > > > ----------------------------------------------------------------------------- > Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu > Emeritus Professor of Chemistry Cell: 617-775-9915 > Boston College www2.bc.edu/evan-kantrowitz -----------------------------------------------------------------------------

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ChimeraX-1.8 functionality regarding the match command
by Nicholas Ferraro 02 Dec '24

02 Dec '24

Good morning, My name is Nicholas Ferraro. I am a graduate student at the City College of New York. I am currently using ChimeraX-1.8 to visualize multiple PDBs of the hexameric helicase I am working with. We have labeled each protomer of the hexamer A-F. I understand the software allows for matching structures either by best-aligning pair of chains, a specific reference structure to the best-aligning chain, and specific chains in a reference structure with specific chains in the matching chain. I have six PDBs. What I want to do is align all chains with respect to their chain ID and specific sequence. Can you advise on how to accomplish this in chimera-1.8? Thank you for you assistance. Please let me know if you need more details. Best, Nicholas Ferraro

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