Dear ChimeraX users! I noticed that there is some difference in the quality of the molecular movies produced in Ubuntu or MacOSX environments. Are there some tricks to improve the quality of the animation produced on ubuntu ? Here are the commands which produced the best results: movie record size 1920,1080 supersample 4 movie encode format h264 quality higher bitrate 25000 how could I modify / add something more with the aim to obtain the best molecular animations ?? Yours sincerely Enrico
Hi Enrico, The Mac probably produces a nicer quality video simply because the size is bigger in pixels if your Mac has a 4K or 5K display. If you don't specify a size in pixels for the movie frames with the movie record command then it just uses the size on the screen. So the way to improve quality on a lower resolution display is to specify the movie frame size in pixels as in your example with the movie record command. You can make it bigger than 1920 by 1080 -- software that plays it back will scale it down to fit the playback window. I would not recommend "supersample 4" as that is going to make image capture 16 times slower. Usually I use no supersample, but if you like the little bit of smoothing it offers than use "supersample 3" (9 times slower image saving), you won't notice any difference with supersample 4. Read the documentation. Your use of the movie encode command with the bitrate option has no effect because the quality option overrides it. As it says in the docs: https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode "When specified by the user, quality overrides qscale and bitrate (constant bit rate encoding)." So use "quality highest" or "bitrate 25000" but not both. One last suggestions is that if you are making your animation on a white background enable silhouette edges (in graphics toolbar), it gives a nicer appearance of the boundaries of objects. Tom
On Jan 30, 2024, at 6:36 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
I noticed that there is some difference in the quality of the molecular movies produced in Ubuntu or MacOSX environments.
Are there some tricks to improve the quality of the animation produced on ubuntu ? Here are the commands which produced the best results:
movie record size 1920,1080 supersample 4 movie encode format h264 quality higher bitrate 25000
how could I modify / add something more with the aim to obtain the best molecular animations ??
Yours sincerely
Enrico _______________________________________________ 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/
Okay, thank you very much Tom ! With best wishes, Enrico Il giorno mar 30 gen 2024 alle ore 19:55 Tom Goddard <goddard@sonic.net> ha scritto:
Hi Enrico,
The Mac probably produces a nicer quality video simply because the size is bigger in pixels if your Mac has a 4K or 5K display. If you don't specify a size in pixels for the movie frames with the movie record command then it just uses the size on the screen.
So the way to improve quality on a lower resolution display is to specify the movie frame size in pixels as in your example with the movie record command. You can make it bigger than 1920 by 1080 -- software that plays it back will scale it down to fit the playback window. I would not recommend "supersample 4" as that is going to make image capture 16 times slower. Usually I use no supersample, but if you like the little bit of smoothing it offers than use "supersample 3" (9 times slower image saving), you won't notice any difference with supersample 4.
Read the documentation. Your use of the movie encode command with the bitrate option has no effect because the quality option overrides it. As it says in the docs:
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode
"When specified by the user, quality overrides qscale and bitrate (constant bit rate encoding)."
So use "quality highest" or "bitrate 25000" but not both.
One last suggestions is that if you are making your animation on a white background enable silhouette edges (in graphics toolbar), it gives a nicer appearance of the boundaries of objects.
Tom
On Jan 30, 2024, at 6:36 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
I noticed that there is some difference in the quality of the molecular movies produced in Ubuntu or MacOSX environments.
Are there some tricks to improve the quality of the animation produced on ubuntu ? Here are the commands which produced the best results:
movie record size 1920,1080 supersample 4 movie encode format h264 quality higher bitrate 25000
how could I modify / add something more with the aim to obtain the best molecular animations ??
Yours sincerely
Enrico _______________________________________________ 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/
One more question about movie making in Chimera-X Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 . Many thanks in advance Enrico Il giorno mer 31 gen 2024 alle ore 09:49 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Okay, thank you very much Tom !
With best wishes,
Enrico
Il giorno mar 30 gen 2024 alle ore 19:55 Tom Goddard <goddard@sonic.net> ha scritto:
Hi Enrico,
The Mac probably produces a nicer quality video simply because the size is bigger in pixels if your Mac has a 4K or 5K display. If you don't specify a size in pixels for the movie frames with the movie record command then it just uses the size on the screen.
So the way to improve quality on a lower resolution display is to specify the movie frame size in pixels as in your example with the movie record command. You can make it bigger than 1920 by 1080 -- software that plays it back will scale it down to fit the playback window. I would not recommend "supersample 4" as that is going to make image capture 16 times slower. Usually I use no supersample, but if you like the little bit of smoothing it offers than use "supersample 3" (9 times slower image saving), you won't notice any difference with supersample 4.
Read the documentation. Your use of the movie encode command with the bitrate option has no effect because the quality option overrides it. As it says in the docs:
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode
"When specified by the user, quality overrides qscale and bitrate (constant bit rate encoding)."
So use "quality highest" or "bitrate 25000" but not both.
One last suggestions is that if you are making your animation on a white background enable silhouette edges (in graphics toolbar), it gives a nicer appearance of the boundaries of objects.
Tom
On Jan 30, 2024, at 6:36 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users!
I noticed that there is some difference in the quality of the molecular movies produced in Ubuntu or MacOSX environments.
Are there some tricks to improve the quality of the animation produced on ubuntu ? Here are the commands which produced the best results:
movie record size 1920,1080 supersample 4 movie encode format h264 quality higher bitrate 25000
how could I modify / add something more with the aim to obtain the best molecular animations ??
Yours sincerely
Enrico _______________________________________________ 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/
Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g. coordset #4 10000,1,-1 where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
Thank you very much, Elaine ! All the best, Enrico Il giorno ven 2 feb 2024 alle ore 17:14 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
Just another question about movie making in the Chimera-X. Assuming that I've loaded all the frames from the pdb using open ./my.pdb coordset true and set up all the graphical options for this trajectory. would it be possible to load another pdb file (as the second part of the same trajectory) in the current session, just adding additional frames without alterations of the orientation of the object displayed in the graphical window ? Many thanks in advance ! Enrico Il giorno ven 2 feb 2024 alle ore 17:19 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Thank you very much, Elaine !
All the best,
Enrico
Il giorno ven 2 feb 2024 alle ore 17:14 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
P.S. I also have one more question about the movie record Would it be possible to select different raytracing modes during the movie recording with the aim to add some elements of "cartoon animation" to the final story ? E.g. while recording the movie using movie record / encode I found that the silhouettes have almost disappeared while I do see them in the current GUI during recording ... Also the surfaces looks abit different on video compared to what I see in the final movie (abit plastic look) Many thanks in advance!! Il giorno lun 5 feb 2024 alle ore 09:42 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Just another question about movie making in the Chimera-X.
Assuming that I've loaded all the frames from the pdb using
open ./my.pdb coordset true
and set up all the graphical options for this trajectory.
would it be possible to load another pdb file (as the second part of the same trajectory) in the current session, just adding additional frames without alterations of the orientation of the object displayed in the graphical window ?
Many thanks in advance !
Enrico
Il giorno ven 2 feb 2024 alle ore 17:19 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Thank you very much, Elaine !
All the best,
Enrico
Il giorno ven 2 feb 2024 alle ore 17:14 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
You can adjust the display to your preferred appearance beforehand with many "graphics" and "lighting" command options (e.g. "graphics silhouettes" has a "width" option), see the help pages for those commands. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> I don't know what you mean by cartoon animation, but there are also "cartoon style" options that you can set before movie recording and/or change during the movie. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html> However, the loss of quality may be in the movie encoding stage (when it converts from individual images to the movie file) so you may need to also try different "movie encode" options. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode> 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, 2024, at 7:52 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
P.S. I also have one more question about the movie record Would it be possible to select different raytracing modes during the movie recording with the aim to add some elements of "cartoon animation" to the final story ? E.g. while recording the movie using movie record / encode I found that the silhouettes have almost disappeared while I do see them in the current GUI during recording ... Also the surfaces looks abit different on video compared to what I see in the final movie (abit plastic look)
Many thanks in advance!!
Il giorno lun 5 feb 2024 alle ore 09:42 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Just another question about movie making in the Chimera-X.
Assuming that I've loaded all the frames from the pdb using
open ./my.pdb coordset true
and set up all the graphical options for this trajectory.
would it be possible to load another pdb file (as the second part of the same trajectory) in the current session, just adding additional frames without alterations of the orientation of the object displayed in the graphical window ?
Many thanks in advance !
Enrico
Il giorno ven 2 feb 2024 alle ore 17:19 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Thank you very much, Elaine !
All the best,
Enrico
Il giorno ven 2 feb 2024 alle ore 17:14 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
Thank you very much Elaine ! I actually do encoding in the highest quality in the h264 format, and for a movie of 2 mins (around 3000 frames) usually it takes around 1-2 mins so much faster compared to the recording. All the best Enrico Il giorno lun 5 feb 2024 alle ore 17:21 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
You can adjust the display to your preferred appearance beforehand with many "graphics" and "lighting" command options (e.g. "graphics silhouettes" has a "width" option), see the help pages for those commands.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html>
I don't know what you mean by cartoon animation, but there are also "cartoon style" options that you can set before movie recording and/or change during the movie.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>
However, the loss of quality may be in the movie encoding stage (when it converts from individual images to the movie file) so you may need to also try different "movie encode" options.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode>
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, 2024, at 7:52 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
P.S. I also have one more question about the movie record Would it be possible to select different raytracing modes during the movie recording with the aim to add some elements of "cartoon animation" to the final story ? E.g. while recording the movie using movie record / encode I found that the silhouettes have almost disappeared while I do see them in the current GUI during recording ... Also the surfaces looks abit different on video compared to what I see in the final movie (abit plastic look)
Many thanks in advance!!
Il giorno lun 5 feb 2024 alle ore 09:42 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Just another question about movie making in the Chimera-X.
Assuming that I've loaded all the frames from the pdb using
open ./my.pdb coordset true
and set up all the graphical options for this trajectory.
would it be possible to load another pdb file (as the second part of the same trajectory) in the current session, just adding additional frames without alterations of the orientation of the object displayed in the graphical window ?
Many thanks in advance !
Enrico
Il giorno ven 2 feb 2024 alle ore 17:19 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Thank you very much, Elaine !
All the best,
Enrico
Il giorno ven 2 feb 2024 alle ore 17:14 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
Going back to my first question: would it be possible to load additional frames in the current session using open .pdb coordset true command ? or alternatively I need to do it from the beginning? Il giorno lun 5 feb 2024 alle ore 17:43 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Thank you very much Elaine !
I actually do encoding in the highest quality in the h264 format, and for a movie of 2 mins (around 3000 frames) usually it takes around 1-2 mins so much faster compared to the recording.
All the best
Enrico
Il giorno lun 5 feb 2024 alle ore 17:21 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
You can adjust the display to your preferred appearance beforehand with many "graphics" and "lighting" command options (e.g. "graphics silhouettes" has a "width" option), see the help pages for those commands.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html>
I don't know what you mean by cartoon animation, but there are also "cartoon style" options that you can set before movie recording and/or change during the movie.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html>
However, the loss of quality may be in the movie encoding stage (when it converts from individual images to the movie file) so you may need to also try different "movie encode" options.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html#encode>
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, 2024, at 7:52 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
P.S. I also have one more question about the movie record Would it be possible to select different raytracing modes during the movie recording with the aim to add some elements of "cartoon animation" to the final story ? E.g. while recording the movie using movie record / encode I found that the silhouettes have almost disappeared while I do see them in the current GUI during recording ... Also the surfaces looks abit different on video compared to what I see in the final movie (abit plastic look)
Many thanks in advance!!
Il giorno lun 5 feb 2024 alle ore 09:42 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Just another question about movie making in the Chimera-X.
Assuming that I've loaded all the frames from the pdb using
open ./my.pdb coordset true
and set up all the graphical options for this trajectory.
would it be possible to load another pdb file (as the second part of the same trajectory) in the current session, just adding additional frames without alterations of the orientation of the object displayed in the graphical window ?
Many thanks in advance !
Enrico
Il giorno ven 2 feb 2024 alle ore 17:19 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Thank you very much, Elaine !
All the best,
Enrico
Il giorno ven 2 feb 2024 alle ore 17:14 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: > > One more question about movie making in Chimera-X > > Is there some possibility to record molecular movie in the reverse > order from a given multi-model pdb file ? > E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 . > > Many thanks in advance > > Enrico
Silhouette edges have a width in pixels, usually 1 pixel. If you record a movie and specify a larger image size (e.g. 1920 x 1080) than what you see on your screen (e.g. 800 x 600) then the silhouettes will look thinner in the movie. You can specify the silhouette thickness in pixels with this command graphics silhouette width 3 ChimeraX does not do raytracing. It has different lighting modes. Tom
On Feb 5, 2024, at 7:52 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
P.S. I also have one more question about the movie record Would it be possible to select different raytracing modes during the movie recording with the aim to add some elements of "cartoon animation" to the final story ? E.g. while recording the movie using movie record / encode I found that the silhouettes have almost disappeared while I do see them in the current GUI during recording ... Also the surfaces looks abit different on video compared to what I see in the final movie (abit plastic look)
Many thanks in advance!!
Il giorno lun 5 feb 2024 alle ore 09:42 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Just another question about movie making in the Chimera-X.
Assuming that I've loaded all the frames from the pdb using
open ./my.pdb coordset true
and set up all the graphical options for this trajectory.
would it be possible to load another pdb file (as the second part of the same trajectory) in the current session, just adding additional frames without alterations of the orientation of the object displayed in the graphical window ?
Many thanks in advance !
Enrico
Il giorno ven 2 feb 2024 alle ore 17:19 Enrico Martinez <jmsstarlight@gmail.com> ha scritto:
Thank you very much, Elaine !
All the best,
Enrico
Il giorno ven 2 feb 2024 alle ore 17:14 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
_______________________________________________ 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/
Just to precise :: *Coordset #1 -1,1,-1* Would this play the movie backwards from the last to the first frame ? ( so in this case I do not precise explicitly the number of the last frame) Alternatively *Coordset #1 1,-1,1* Plays the trajectory from the beginning to the end , doesn’t it ? Many thanks in advance !! Le ven. 2 févr. 2024 à 17:14, Elaine Meng <meng@cgl.ucsf.edu> a écrit :
Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
You could just try it to see for yourself, but yes and yes. As described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> coordset #1 -1 ...goes to the last frame, so your commands act as you describe. Elaine
On Feb 22, 2024, at 10:33 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Just to precise ::
Coordset #1 -1,1,-1
Would this play the movie backwards from the last to the first frame ? ( so in this case I do not precise explicitly the number of the last frame)
Alternatively
Coordset #1 1,-1,1
Plays the trajectory from the beginning to the end , doesn’t it ?
Many thanks in advance !!
Le ven. 2 févr. 2024 à 17:14, Elaine Meng <meng@cgl.ucsf.edu> a écrit : Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
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/
Okay, thank you very much Elaine ! Actually I tried to decompose my question regarding the automatization of the movie recording in ChimeraX. For example if I do the following script: # MAKE MOVIE WITH CHIMERA-X # start recording movie record size 3840,2160 supersample 1 # play reverse movie: from the end to beginning coordset #1 -1,1,-1 # encode the results movie encode format h264 quality highest output /home/enrico/PRIVATE/test_movie.mp4 so If I execute this script, the chimera-X will sends me an error that there are no frames to encode since it tries to run all commands at the same time. Alternatively I may add WAIT just before the movie encode, but in this case I need to explicitly define the period (e.g. wait 20). Would it be possible rather to insert this pause w*ithout the** explicit definition of the period* (untull he coordset reaches the first frame ) ? Many thanks in advance Enrico Il giorno gio 22 feb 2024 alle ore 20:17 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
You could just try it to see for yourself, but yes and yes.
As described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
coordset #1 -1
...goes to the last frame, so your commands act as you describe.
Elaine
On Feb 22, 2024, at 10:33 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Just to precise ::
Coordset #1 -1,1,-1
Would this play the movie backwards from the last to the first frame ? ( so in this case I do not precise explicitly the number of the last frame)
Alternatively
Coordset #1 1,-1,1
Plays the trajectory from the beginning to the end , doesn’t it ?
Many thanks in advance !!
Le ven. 2 févr. 2024 à 17:14, Elaine Meng <meng@cgl.ucsf.edu> a écrit : Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
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/
As far as I know, you need to give the number of frames. Instead of trying to make a generic command script that will cover all your of your different movies of different lengths, you may need to also use python that determines the number of frames in each specific case. Somebody else would have to help with that, however, as I don't know python. Elaine
On Feb 23, 2024, at 12:38 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Okay, thank you very much Elaine !
Actually I tried to decompose my question regarding the automatization of the movie recording in ChimeraX.
For example if I do the following script:
# MAKE MOVIE WITH CHIMERA-X # start recording movie record size 3840,2160 supersample 1 # play reverse movie: from the end to beginning coordset #1 -1,1,-1
# encode the results movie encode format h264 quality highest output /home/enrico/PRIVATE/test_movie.mp4
so If I execute this script, the chimera-X will sends me an error that there are no frames to encode since it tries to run all commands at the same time. Alternatively I may add WAIT just before the movie encode, but in this case I need to explicitly define the period (e.g. wait 20).
Would it be possible rather to insert this pause without the explicit definition of the period (untull he coordset reaches the first frame ) ?
Many thanks in advance
Enrico
Il giorno gio 22 feb 2024 alle ore 20:17 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: You could just try it to see for yourself, but yes and yes.
As described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
coordset #1 -1
...goes to the last frame, so your commands act as you describe.
Elaine
On Feb 22, 2024, at 10:33 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Just to precise ::
Coordset #1 -1,1,-1
Would this play the movie backwards from the last to the first frame ? ( so in this case I do not precise explicitly the number of the last frame)
Alternatively
Coordset #1 1,-1,1
Plays the trajectory from the beginning to the end , doesn’t it ?
Many thanks in advance !!
Le ven. 2 févr. 2024 à 17:14, Elaine Meng <meng@cgl.ucsf.edu> a écrit : Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
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/
You need to put a wait command before you do the movie encode command. Only the wait command causes frames to be rendered. So if you want to render 300 frames you have to add wait 300 after the coordset command. Tom
On Feb 23, 2024, at 8:22 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
As far as I know, you need to give the number of frames. Instead of trying to make a generic command script that will cover all your of your different movies of different lengths, you may need to also use python that determines the number of frames in each specific case. Somebody else would have to help with that, however, as I don't know python.
Elaine
On Feb 23, 2024, at 12:38 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Okay, thank you very much Elaine !
Actually I tried to decompose my question regarding the automatization of the movie recording in ChimeraX.
For example if I do the following script:
# MAKE MOVIE WITH CHIMERA-X # start recording movie record size 3840,2160 supersample 1 # play reverse movie: from the end to beginning coordset #1 -1,1,-1
# encode the results movie encode format h264 quality highest output /home/enrico/PRIVATE/test_movie.mp4
so If I execute this script, the chimera-X will sends me an error that there are no frames to encode since it tries to run all commands at the same time. Alternatively I may add WAIT just before the movie encode, but in this case I need to explicitly define the period (e.g. wait 20).
Would it be possible rather to insert this pause without the explicit definition of the period (untull he coordset reaches the first frame ) ?
Many thanks in advance
Enrico
Il giorno gio 22 feb 2024 alle ore 20:17 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: You could just try it to see for yourself, but yes and yes.
As described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
coordset #1 -1
...goes to the last frame, so your commands act as you describe.
Elaine
On Feb 22, 2024, at 10:33 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Just to precise ::
Coordset #1 -1,1,-1
Would this play the movie backwards from the last to the first frame ? ( so in this case I do not precise explicitly the number of the last frame)
Alternatively
Coordset #1 1,-1,1
Plays the trajectory from the beginning to the end , doesn’t it ?
Many thanks in advance !!
Le ven. 2 févr. 2024 à 17:14, Elaine Meng <meng@cgl.ucsf.edu> a écrit : Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
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/
_______________________________________________ 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/
Thank you very much Tom ! Actually I did not know that the argument provided for Wait command corresponds to the number of frames ( I thought it was rather a pause in seconds ... ) Yours with thanks Enrico Il giorno ven 23 feb 2024 alle ore 18:15 Tom Goddard <goddard@sonic.net> ha scritto:
You need to put a wait command before you do the movie encode command. Only the wait command causes frames to be rendered. So if you want to render 300 frames you have to add
wait 300
after the coordset command.
Tom
On Feb 23, 2024, at 8:22 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
As far as I know, you need to give the number of frames. Instead of trying to make a generic command script that will cover all your of your different movies of different lengths, you may need to also use python that determines the number of frames in each specific case. Somebody else would have to help with that, however, as I don't know python.
Elaine
On Feb 23, 2024, at 12:38 AM, Enrico Martinez <jmsstarlight@gmail.com> wrote:
Okay, thank you very much Elaine !
Actually I tried to decompose my question regarding the automatization of the movie recording in ChimeraX.
For example if I do the following script:
# MAKE MOVIE WITH CHIMERA-X # start recording movie record size 3840,2160 supersample 1 # play reverse movie: from the end to beginning coordset #1 -1,1,-1
# encode the results movie encode format h264 quality highest output /home/enrico/PRIVATE/test_movie.mp4
so If I execute this script, the chimera-X will sends me an error that there are no frames to encode since it tries to run all commands at the same time. Alternatively I may add WAIT just before the movie encode, but in this case I need to explicitly define the period (e.g. wait 20).
Would it be possible rather to insert this pause without the explicit definition of the period (untull he coordset reaches the first frame ) ?
Many thanks in advance
Enrico
Il giorno gio 22 feb 2024 alle ore 20:17 Elaine Meng <meng@cgl.ucsf.edu> ha scritto: You could just try it to see for yourself, but yes and yes.
As described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
coordset #1 -1
...goes to the last frame, so your commands act as you describe.
Elaine
On Feb 22, 2024, at 10:33 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Just to precise ::
Coordset #1 -1,1,-1
Would this play the movie backwards from the last to the first frame ? ( so in this case I do not precise explicitly the number of the last frame)
Alternatively
Coordset #1 1,-1,1
Plays the trajectory from the beginning to the end , doesn’t it ?
Many thanks in advance !!
Le ven. 2 févr. 2024 à 17:14, Elaine Meng <meng@cgl.ucsf.edu> a écrit : Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
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/
_______________________________________________ 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 Enrico, The wait command needs the number of frames to wait when used with the coordset command. For a few other commands (turn, move, roll) the wait command can be used without any arguments and it waits until they finish, but that is only for a few commands and does not work with coordset. Sorry for the delayed reply. I think you sent this question a few weeks ago but it did not get delivered until today due to problems with our mailing list software. Tom
On Feb 23, 2024, at 12:38 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Okay, thank you very much Elaine !
Actually I tried to decompose my question regarding the automatization of the movie recording in ChimeraX.
For example if I do the following script:
# MAKE MOVIE WITH CHIMERA-X # start recording movie record size 3840,2160 supersample 1 # play reverse movie: from the end to beginning coordset #1 -1,1,-1
# encode the results movie encode format h264 quality highest output /home/enrico/PRIVATE/test_movie.mp4
so If I execute this script, the chimera-X will sends me an error that there are no frames to encode since it tries to run all commands at the same time. Alternatively I may add WAIT just before the movie encode, but in this case I need to explicitly define the period (e.g. wait 20).
Would it be possible rather to insert this pause without the explicit definition of the period (untull he coordset reaches the first frame ) ?
Many thanks in advance
Enrico
Il giorno gio 22 feb 2024 alle ore 20:17 Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> ha scritto:
You could just try it to see for yourself, but yes and yes.
As described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
coordset #1 -1
...goes to the last frame, so your commands act as you describe.
Elaine
On Feb 22, 2024, at 10:33 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
Just to precise ::
Coordset #1 -1,1,-1
Would this play the movie backwards from the last to the first frame ? ( so in this case I do not precise explicitly the number of the last frame)
Alternatively
Coordset #1 1,-1,1
Plays the trajectory from the beginning to the end , doesn’t it ?
Many thanks in advance !!
Le ven. 2 févr. 2024 à 17:14, Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> a écrit : Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
_______________________________________________ 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/
No problem, thank you for your response Tom ! Have a great day Enrico Il giorno mar 5 mar 2024 alle ore 01:36 Tom Goddard <goddard@sonic.net> ha scritto:
Hi Enrico,
The wait command needs the number of frames to wait when used with the coordset command. For a few other commands (turn, move, roll) the wait command can be used without any arguments and it waits until they finish, but that is only for a few commands and does not work with coordset.
Sorry for the delayed reply. I think you sent this question a few weeks ago but it did not get delivered until today due to problems with our mailing list software.
Tom
On Feb 23, 2024, at 12:38 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Okay, thank you very much Elaine !
Actually I tried to decompose my question regarding the automatization of the movie recording in ChimeraX.
For example if I do the following script:
# MAKE MOVIE WITH CHIMERA-X # start recording movie record size 3840,2160 supersample 1 # play reverse movie: from the end to beginning coordset #1 -1,1,-1
# encode the results movie encode format h264 quality highest output /home/enrico/PRIVATE/test_movie.mp4
so If I execute this script, the chimera-X will sends me an error that there are no frames to encode since it tries to run all commands at the same time. Alternatively I may add WAIT just before the movie encode, but in this case I need to explicitly define the period (e.g. wait 20).
Would it be possible rather to insert this pause w*ithout the** explicit definition of the period* (untull he coordset reaches the first frame ) ?
Many thanks in advance
Enrico
Il giorno gio 22 feb 2024 alle ore 20:17 Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
You could just try it to see for yourself, but yes and yes.
As described in the help: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>
coordset #1 -1
...goes to the last frame, so your commands act as you describe.
Elaine
On Feb 22, 2024, at 10:33 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Just to precise ::
Coordset #1 -1,1,-1
Would this play the movie backwards from the last to the first frame ? ( so in this case I do not precise explicitly the number of the last frame)
Alternatively
Coordset #1 1,-1,1
Plays the trajectory from the beginning to the end , doesn’t it ?
Many thanks in advance !!
Le ven. 2 févr. 2024 à 17:14, Elaine Meng <meng@cgl.ucsf.edu> a écrit : Yes, you can simply use the "coordset" command to play the trajectory in reverse by specifying a negative step, e.g.
coordset #4 10000,1,-1
where as the help page says, #4 is the trajectory model number, 10000 is the trajectory frame to start, 1 is the trajectory frame to end, -1 is the step. Please see the page:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.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 2, 2024, at 5:40 AM, Enrico Martinez via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
One more question about movie making in Chimera-X
Is there some possibility to record molecular movie in the reverse order from a given multi-model pdb file ? E.g. having 1000 models, I would like to record it from 1000,999,998 ... 1 .
Many thanks in advance
Enrico
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/
_______________________________________________ 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/
participants (3)
-
Elaine Meng -
Enrico Martinez -
Tom Goddard