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,
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German Barcenas
Ph.D Candidate | Materials Science and Engineering
Materials Modeling and Theory Group
Boise State University