Recording MD Trajectory Movie in ChimeraX
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 --
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--
Hi Gourav, I forgot to mention: If you would rather not create a command file, you can record a very simple movie of the trajectory playback with the "record" (red dot) button on the slider graphical interface that automatically appears when you open the trajectory. The slider interface is described here: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider> The command-file approach is for when you want to do fancier things like rotations and changes in appearance, and have labels appear and disappear. I hope this helps, Elaine
On Feb 5, 2025, at 8:48 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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--
_______________________________________________ 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/
Dear Elaine, Thank you very much for your kind assistance. Can you kindly guide me to improve the resolution of the movie? With regards, Gourav Das On Thu, Feb 6, 2025 at 1:03 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Gourav, I forgot to mention:
If you would rather not create a command file, you can record a very simple movie of the trajectory playback with the "record" (red dot) button on the slider graphical interface that automatically appears when you open the trajectory. The slider interface is described here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider>
The command-file approach is for when you want to do fancier things like rotations and changes in appearance, and have labels appear and disappear.
I hope this helps, Elaine
On Feb 5, 2025, at 8:48 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
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--
_______________________________________________ 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/
Hi Gourav, You do not have access to options if you just click the movie record button, sorry. However, you can resize the whole window bigger beforehand, if that is what you mean. If you want to use the "movie" command options it will be necessary to use the commands approach. The "movie record" command options include "size" "supersample" etc. and "movie encode" options include "quality" etc. all explained in the help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html> See the "making movies" page including links to tutorials therein: <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 5, 2025, at 10:15 PM, Gourav Das via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thank you very much for your kind assistance. Can you kindly guide me to improve the resolution of the movie?
With regards, Gourav Das
On Thu, Feb 6, 2025 at 1:03 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Gourav, I forgot to mention:
If you would rather not create a command file, you can record a very simple movie of the trajectory playback with the "record" (red dot) button on the slider graphical interface that automatically appears when you open the trajectory. The slider interface is described here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider>
The command-file approach is for when you want to do fancier things like rotations and changes in appearance, and have labels appear and disappear.
I hope this helps, Elaine
On Feb 5, 2025, at 8:48 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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--
Dear Elaine, Thanks a lot for your kind help! With regards, Gourav Das On Thu, Feb 6, 2025 at 10:24 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Gourav, You do not have access to options if you just click the movie record button, sorry. However, you can resize the whole window bigger beforehand, if that is what you mean.
If you want to use the "movie" command options it will be necessary to use the commands approach. The "movie record" command options include "size" "supersample" etc. and "movie encode" options include "quality" etc. all explained in the help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html>
See the "making movies" page including links to tutorials therein: <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 5, 2025, at 10:15 PM, Gourav Das via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Dear Elaine,
Thank you very much for your kind assistance. Can you kindly guide me to improve the resolution of the movie?
With regards, Gourav Das
On Thu, Feb 6, 2025 at 1:03 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Gourav, I forgot to mention:
If you would rather not create a command file, you can record a very simple movie of the trajectory playback with the "record" (red dot) button on the slider graphical interface that automatically appears when you open the trajectory. The slider interface is described here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider>
The command-file approach is for when you want to do fancier things like rotations and changes in appearance, and have labels appear and disappear.
I hope this helps, Elaine
On Feb 5, 2025, at 8:48 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
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--
participants (2)
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Elaine Meng -
Gourav Das