Hi Yishai, For most trajectories this wouldn’t be feasible, but if your trajectory really is only 100 frames of 8094 atoms each, then an alternative is to open each frame as a separate model — so just omit the "coord T” in your open command. The first frame will be model 1.1, the second model 1.2, etc. You could then align them all with “mmaker #1.2-end to #1.1”, and play through them with the mseries command (e.g. mseries slider #1) [mseries documentation: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html] <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/mseries.html%5D>. For any kind of larger trajectory you would begin to run into performance / memory usage issues. There may even be issues for a trajectory of your size, but my guess is that it will work okay. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Aug 15, 2024, at 5:43 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Yishai, Welcome to ChimeraX!
Yes, it sounds like what you want is the "holdsteady" option of "coordset" -- note that this does not change your trajectory coordinates, but in each frame update, the specified atoms are fit onto the previous locations so that they appear to be in the same place as much as possible. They are not absolutely fixed in place since their spatial relationships might be different within different frames, but the frame is basically fit to the previous frame using those atoms.
There is no syntax for specifying the different frames of a trajectory, as they do not exist at the same time as each other. Therefore, you cannot use other commands like "matchmaker" or "align." There are other programs (outside of ChimeraX) that you could use to process your trajectory beforehand to remove rotations and translations, actually changing the trajectory coordinates, if you can't get what you want "on the fly" using ChimeraX coordset with holdsteady. I'm not an expert in that area, however, so I don't have a specific recommendation.
The "coordset" command actually plays the trajectory. So your example plays frames 1-100 while applying holdsteady on the CA atoms. You can use other atoms if you want (e.g. a whole residue, or all backbone, etc.). The holdsteady option doesn't change the trajectory, so if you play it again without using holdsteady, nothing is held steady. You would have to use it every time you play back the trajectory with "coordset."
coordset help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
I hope this makes sense, 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 Aug 15, 2024, at 5:25 PM, ygilron--- via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi I am new to UCSF ChimeraX, and would like to learn how to use it for visualizing trajectories. Previously, I was using pymol for this, but would like to use ChimeraX's better image rendering for a publication.
I was able to load the .pdb file of my trajectory with: open <"path/to/pdb"> format pdb coord T
Currently, this is the info of my file:
info 1 models #1, lambda25_trajectory_1k_res.pdb, shown 8094 atoms, 8219 bonds, 514 residues, 1 chains ( ), 100 coordsets
I would like to remove translations and rotations by fitting each frame with a command similar to 'align': align matchatoms toAtoms refatoms [ cutoffDistance d ] [ move what ] [ each level ] [ reportMatrix true | false ] pairing-options Although, it seems I would have to do this manually 99 times for each pair of coordsets of the trajectory.
Additionally, I am not sure I have the correct syntax for choosing a coordset from a model: align #1 , 1 toAtoms #1 ,2 gave me the following output: align #1 , 1 toAtoms #1 ,2RMSD between 8094 atom pairs is 0.000 angstroms That probably shouldn't be that accurate, right?
In PyMOL one would use the command: intra_fit <model name> in order to do this.
The best I was able to deduce was the following command: coordset #1 1,100 holdSteady @ca I am not sure if this is doing the same thing (rmsd fitting of model #1 coordset 1 to model #1 coordset 2.... ....model #1 coordset 99 to model #1 coordset 100 ) but rather just fixing the C-alpha atoms in place? is this equivalent?
Also, I noticed this only aligns the coordsets once, and then reverts back to the default trajectory of tumbling around with all the rotations and translations. How can I set this holdSteady to be permanent for all future plays of my trajectory? Best, Yishai
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