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: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/