Viewing all frames of trajectory at once
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
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@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,
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@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@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@u.boisestate.edu | 940-577-5094
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Elaine Meng -
German Barcenas