[chimerax-users] Viewing all frames of trajectory at once

[German Barcenas]

Ohh okay yes that multi-frame pdb workflow makes sense to me. Thank you!

On Wed, Nov 17, 2021 at 2:13 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello German,
> When the coordinate sets are loaded as a trajectory, you can only view one
> frame at a time.
>
> However, after opening your trajectory, you can:
>
> (1) save it as a multi-model PDB file, e.g. if the trajectory is model #1,
> command:
> save myfile.pdb models #1 allCoordsets true
>
> see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb>
>
> (2) close the trajectory, open the multi-model PDB file
> By default it will not be treated as a trajectory but as separate models
> all shown at once (e.g. if the file is opened as #1, you can disclose in
> the Model Panel that the individual ones are #1.1, #1.2, ..... however many
> frames were in the trajectory)
>
> (3) use the transparency command only on the specific model(s) that you
> want to be transparent, e.g. command:
> transparency #1.2-10 75 target ar
>
> see <https://rbvi.ucsf.edu/chimerax/docs/user/commands/transparency.html>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Nov 17, 2021, at 11:57 AM, German Barcenas via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
> >
> > Hello,
> > I've made a trajectory of some similar frames that are stored as an .xtc
> file. I can upload this with my defined topology file (.pdb) and see each
> frame individually. Currently I can create a picture of each frame with the
> frame centered on some residue (SQA) with:
> >
> > perframe "save ~\snapshot_$1.png"  frames 10;coordset #1 holdSteady
> /A:SQA
> >
> > This creates individual pictures for each frame which is nice. I was
> wondering how one makes a picture with all 10 frames superimposed on each
> other. I'd also like to change all but the 1st frame to be transparent. I'm
> aware of the transparent command, which I presume I'd apply to all frames
> except the 1st, but I'm not sure how to display all frames at once. I'm
> also struggling on the 1st frame only condition. This is my current attempt:
> >
> > perframe "transparency 0 ALL"  frames 1;perframe "transparency 25 ALL"
> frames 9;coordset #1 holdSteady /A:SQA
> > Thanks,
>
>

-- 
German Barcenas
Ph.D Candidate | Materials Science and Engineering
Materials Modeling and Theory Group
Boise State University
germanbarcenas at u.boisestate.edu | 940-577-5094
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/attachments/20211117/ee354750/attachment.html>