Thank you for your fast reply! I succeeded in combining the files but then I had 228 k atoms and the xtc.file was for 11383 atoms. It turns out that any of the PDB files that I uploaded, that was generated every 25 picosecond(that way was set in the macro), it worked and it created a movie. Although the pdb structures taken at different time might be different, since I created a movie and selected from frame 1 to the last, in the end they had the same movement. Thank you again for your support ! Kind Regards, Ivan Bogdanov На 2025-03-06 20:00, Eric Pettersen написа:

Hi Ivan, I’m not terribly familiar with YASARA, so I’m not sure if you’re saying: (A) you have a series of PDB files, one per frame, that each have all the atoms of the system; or (B) you have several PDB files, each of which have only some of the atoms of the system. If (A), then you just open the PDB file for the first frame and then the .xtc file, and that loads the trajectory. if (B), then you need to open the PDB files in the same order that the atoms are in the .xtc file, then use the “combine” command to combine them into one model (probably: “combine close true name _what-you-want-the-new-model-named_”), then open the .xtc file to load the trajectory. The PDB files would need to have all the atoms that the .xtc file does.

--Eric

Eric Pettersen UCSF Computer Graphics Lab

...

On Mar 6, 2025, at 7:13 AM, ibogdanov via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi !

I have the following question - How can I create a movie, when I cannot use the YASARA.sce file from which I converted/extracted xtc.file(the trajectories) when I have all the snapshots(pdb and sim.files) created as separate files during the performed simulation in YASARA...I've uploaded for example the first pdb file of the series and the xtc.file but isn't the saved xtc.file(trajectories) of the whole simulation(for all the structures)?

How would you suggest me to solve this problem, if ChimeraX doesn't support sce.files ?

Thank you in advance!

Kind Regards, Ivan Bogdanov _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives:

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