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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>
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>

(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>
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>

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>

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 --------------
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>
> 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 --------------
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>
>
> -----------------------------------------------------------------------------
> 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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End of ChimeraX-users Digest, Vol 96, Issue 1
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