Hi everyone! I am missing a way to add/edit chain descriptions in ChimeraX. Is it possible? If not, would this be a reasonable request to plan for a future release? Wishing a nice day to whoever reads this message =) André ________________________________ From: chimerax-users-request@cgl.ucsf.edu <chimerax-users-request@cgl.ucsf.edu> Sent: Monday, December 2, 2024 10:52 PM To: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 96, Issue 1 Send ChimeraX-users mailing list submissions to chimerax-users@cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request@cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner@cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change. (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 2 Dec 2024 13:52:23 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change. To: Evan Kantrowitz <kantrow@bc.edu> Cc: Eric Pettersen via Chimera-users <chimera-users@cgl.ucsf.edu>, chimerax-users <chimerax-users@cgl.ucsf.edu> Message-ID: <0368B293-FF58-4F72-97C0-51DF75D23035@cgl.ucsf.edu> Content-Type: multipart/mixed; boundary="Apple-Mail=_5630A7C6-3B74-4E39-A0F1-3F2D7DF8DDB0" 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@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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fmseries.html&data=05%7C02%7Candre.graca%40umu.se%7Cf207efa33afb4468334c08dd131c3e73%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638687733710811921%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=R27Kg5R4yhJti6DKgJPT3Kli44PPRfvApdwJXslziG8%3D&reserved=0<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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fopen.html%23coordsets&data=05%7C02%7Candre.graca%40umu.se%7Cf207efa33afb4468334c08dd131c3e73%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638687733710827761%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=IpAggYAh9ih5rn2jplMA05pNzdYr4h2%2FPC1J7dXA79I%3D&reserved=0<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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fcoordset.html&data=05%7C02%7Candre.graca%40umu.se%7Cf207efa33afb4468334c08dd131c3e73%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638687733710835984%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=x7ecOONSwaXV1hchKtHPFoiypkb%2FU%2F8F%2FZDriMwXBXI%3D&reserved=0<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>> More info, general explanation of model series vs. trajectories <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Ftrajectories.html&data=05%7C02%7Candre.graca%40umu.se%7Cf207efa33afb4468334c08dd131c3e73%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638687733710844065%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=ptzZNmnSJGkpO%2Fj6%2BRxX1mCk%2Fo3O0uIwbIa0DFi4OVg%3D&reserved=0<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@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-------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: PastedGraphic-1.png Type: image/png Size: 44782 bytes Desc: not available -------------- next part --------------
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).-------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: PastedGraphic-2.png Type: image/png Size: 113501 bytes Desc: not available -------------- next part --------------
----------------------------------------------------------------------------- Evan R. Kantrowitz, Ph.D evan.kantrowitz@bc.edu Emeritus Professor of Chemistry Cell: 617-775-9915 Boston College www2.bc.edu/evan-kantrowitz -----------------------------------------------------------------------------
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