Re: [Chimera-users] how to play trajectory frames ?
Hi Mitch, What program are you using? It looks like you may be reading the ChimeraX help, but ChimeraX is a different program than Chimera. If you are using ChimeraX, you may want to ask questions on the chimerax-users@cgl.ucsf.edu list and not chimera-users@cgl.ucsf.edu ... We try to keep them separate so that people don't get confused.
Also if you are actually using ChimeraX, the "coordsets" option of "open" is only for opening PDB or mmCIF files, not XTC. Just leave it out, and simply open both the PSF and XTC with the "coords" option similar to the third example in the ChimeraX help section linked below, except that your trajectory file is XTC and not DCD:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options
That just opens the trajectory, it does not play it. To play the trajectory in ChimeraX, you would use the slider GUI and/or the "coordset" command, as mentioned in the help section linked above.
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 Jan 11, 2024, at 3:57 PM, Mitch Murphy via Chimera-users chimera-users@cgl.ucsf.edu wrote:
i tried "open 3ft6.psf coordsets true coords 3ft6.xtc" but i get "'coordsets' has no suffix" error message.
and with "open 3ft6.psf coords 3ft6.xtc coordsets true" i get "Expected a keyword".
how do i play frames of a trajectory. i have the psf and xtc or dcd trajectory files available.
im using chimerax, sorry i sent to wrong list at first.
i tried "open 3ft6.psf slider true coords 3ft6.xtc" and i got error message:
"TypeError: read_coords() got an unexpected keyword argument 'slider'
File "/Applications/ ChimeraX-1.7-rc2023.12.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/md_crds/read_psf.py", line 138, in read_psf read_coords(session, coords, s, data_fmt.nicknames[0], replace=True, **kw)
See log for complete Python traceback."
also i tried "coordset slider" command but i got "*Missing or invalid "structures" argument: empty atom specifier*" error message.
*so please tell me how do i open a trajectory file to play as a movie ?* i dont see a slider gui anywhere in the menus.
On Thu, Jan 11, 2024 at 7:19 PM Elaine Meng meng@cgl.ucsf.edu wrote:
Hi Mitch, What program are you using? It looks like you may be reading the ChimeraX help, but ChimeraX is a different program than Chimera. If you are using ChimeraX, you may want to ask questions on the chimerax-users@cgl.ucsf.edu list and not chimera-users@cgl.ucsf.edu ... We try to keep them separate so that people don't get confused.
Also if you are actually using ChimeraX, the "coordsets" option of "open" is only for opening PDB or mmCIF files, not XTC. Just leave it out, and simply open both the PSF and XTC with the "coords" option similar to the third example in the ChimeraX help section linked below, except that your trajectory file is XTC and not DCD:
https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options
That just opens the trajectory, it does not play it. To play the trajectory in ChimeraX, you would use the slider GUI and/or the "coordset" command, as mentioned in the help section linked above.
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 Jan 11, 2024, at 3:57 PM, Mitch Murphy via Chimera-users <
chimera-users@cgl.ucsf.edu> wrote:
i tried "open 3ft6.psf coordsets true coords 3ft6.xtc" but i get "'coordsets' has no suffix" error message.
and with "open 3ft6.psf coords 3ft6.xtc coordsets true" i get "Expected
a keyword".
how do i play frames of a trajectory. i have the psf and xtc or dcd
trajectory files available.
Hi Mitch, That is a bug with the 'slider' keywords for the PSF format only. I will have that fixed in tomorrow builds. You can work around it right now by omitting the 'slider' part of your 'open' command, and afterward doing "coordset slider #1' (you were missing the "#1" part, and this assumes you opened the trajectory as model 1).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jan 11, 2024, at 4:39 PM, Mitch Murphy via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
im using chimerax, sorry i sent to wrong list at first.
i tried "open 3ft6.psf slider true coords 3ft6.xtc" and i got error message:
"TypeError: read_coords() got an unexpected keyword argument 'slider'
File "/Applications/ChimeraX-1.7-rc2023.12.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/md_crds/read_psf.py http://chimerax-1.7-rc2023.12.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/md_crds/read_psf.py", line 138, in read_psf read_coords(session, coords, s, data_fmt.nicknames[0], replace=True, **kw)
See log for complete Python traceback."
also i tried "coordset slider" command but i got "Missing or invalid "structures" argument: empty atom specifier" error message.
so please tell me how do i open a trajectory file to play as a movie ? i dont see a slider gui anywhere in the menus.
On Thu, Jan 11, 2024 at 7:19 PM Elaine Meng <meng@cgl.ucsf.edu mailto:meng@cgl.ucsf.edu> wrote: Hi Mitch, What program are you using? It looks like you may be reading the ChimeraX help, but ChimeraX is a different program than Chimera. If you are using ChimeraX, you may want to ask questions on the chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu list and not chimera-users@cgl.ucsf.edu mailto:chimera-users@cgl.ucsf.edu ... We try to keep them separate so that people don't get confused.
Also if you are actually using ChimeraX, the "coordsets" option of "open" is only for opening PDB or mmCIF files, not XTC. Just leave it out, and simply open both the PSF and XTC with the "coords" option similar to the third example in the ChimeraX help section linked below, except that your trajectory file is XTC and not DCD:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#traj-options>
That just opens the trajectory, it does not play it. To play the trajectory in ChimeraX, you would use the slider GUI and/or the "coordset" command, as mentioned in the help section linked above.
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 Jan 11, 2024, at 3:57 PM, Mitch Murphy via Chimera-users <chimera-users@cgl.ucsf.edu mailto:chimera-users@cgl.ucsf.edu> wrote:
i tried "open 3ft6.psf coordsets true coords 3ft6.xtc" but i get "'coordsets' has no suffix" error message.
and with "open 3ft6.psf coords 3ft6.xtc coordsets true" i get "Expected a keyword".
how do i play frames of a trajectory. i have the psf and xtc or dcd trajectory files available.
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participants (3)
-
Elaine Meng -
Eric Pettersen -
Mitch Murphy