Hi Gourav, ChimeraX does not read the .parm7 topology file. Instead you need to open a PDB file (like one snapshot from the trajectory) which provides the topology, and then you can open the .nc file with the "open" command as described here. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options> <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.html> Playback of the trajectory is with the "coordset" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> You can put the coordset command and other commands (coloring, style, hide/show, zoom, rotations etc.) into a ChimeraX command script .cxc file, and it can include "movie" commands to start recording, encode the movie, etc. See "making movies" <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> I hope this helps, 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 Feb 4, 2025, at 11:24 PM, Gourav Das via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users,
I have performed MD simulation of a system using AMBER20. The topology and trajectory files are in .parm7 and .nc formats, respectively. I would appreciate your guidance on visualizing and recording the trajectory as a movie in ChimeraX.
Thank you for your support.
With regards,
Gourav Das Research Scholar Department of Chemistry Indian Institute of Technology Kharagpur West Bengal, India-721302 Mob: +91-6295251060--