FYI, this only works completely correctly in the daily build. In the 1.9 release candidate and 1.8 production release you would have to add "create true" to that command. It will also work right in tomorrow's release candidate. --Eric
On Dec 4, 2024, at 12:00 PM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi André, The chain's description is contained in the "description" attribute of a chain, and therefore you can change it with the setattr command. For example, to change the description of chain A in model 1 to be "new description", the command would be:
setattr #1/A c description "new description"
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Dec 4, 2024, at 12:16 AM, André Graça via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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 <mailto:chimerax-users-request@cgl.ucsf.edu> <chimerax-users-request@cgl.ucsf.edu <mailto:chimerax-users-request@cgl.ucsf.edu>> Sent: Monday, December 2, 2024 10:52 PM To: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: ChimeraX-users Digest, Vol 96, Issue 1
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Today's Topics:
1. Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change. (Elaine Meng)
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Message: 1 Date: Mon, 2 Dec 2024 13:52:23 -0800 From: Elaine Meng <meng@cgl.ucsf.edu <mailto: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 <mailto:kantrow@bc.edu>> Cc: Eric Pettersen via Chimera-users <chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>>, chimerax-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Message-ID: <0368B293-FF58-4F72-97C0-51DF75D23035@cgl.ucsf.edu <mailto: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 <mailto: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.... <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.... <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.... <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.... <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 <mailto: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