Hi, I'm trying to create a morphing movie of a series of 3D maps. For that purpose, if I understand correctly, I need a volume series (vseries) of those maps, and according to the documentation (https://www.rbvi.ucsf.edu/chimerax/docs/user/trajectories.html#vseries), I should obtain a volume series simply by opening the maps at once in a file opening dialogue. I attached a screen shot of the Models panel after opening my maps, and my question is, are those maps already consisting a volume series? vseries commands fail with 'No volume series specified' I would appreciate your comments, thank you Best regards, Kotaro
Hi Kotaro, If you want to morph between the maps, in other words interpolate between every pair of maps, then you can just use command volume morph #1-10 more command options here https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph If you don't want to interpolate and just want to show each map in the series then you would be better off opening them as a series since then you will get a slider and play button. Use the "vseries true" option on the open command to tell ChimeraX the maps are a series. open vol_*.mrc vseries true Tom
On Jun 8, 2020, at 6:35 AM, Kotaro TANAKA <kttn8769@gmail.com> wrote:
Hi,
I'm trying to create a morphing movie of a series of 3D maps.
For that purpose, if I understand correctly, I need a volume series (vseries) of those maps, and according to the documentation (https://www.rbvi.ucsf.edu/chimerax/docs/user/trajectories.html#vseries), I should obtain a volume series simply by opening the maps at once in a file opening dialogue.
I attached a screen shot of the Models panel after opening my maps, and my question is, are those maps already consisting a volume series?
vseries commands fail with 'No volume series specified'
I would appreciate your comments, thank you
Best regards,
Kotaro
<chimerax_screen_shot.png>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
On Jun 8, 2020, at 6:35 AM, Kotaro TANAKA <kttn8769@gmail.com> wrote:
I should obtain a volume series simply by opening the maps at once in a file opening dialogue.
To follow up to what Tom wrote, you have to use the ‘open’ command to create a series, you can’t use the open-file dialog. --Eric Eric Pettersen UCSF Computer Graphics Lab
Thank you for your comments,
volume morph #1-10 This is exactly what I wanted. Thank you.
Kotaro On 2020/06/09 0:41, Eric Pettersen wrote:
On Jun 8, 2020, at 6:35 AM, Kotaro TANAKA <kttn8769@gmail.com <mailto:kttn8769@gmail.com>> wrote:
I should obtain a volume series simply by opening the maps at once in a file opening dialogue.
To follow up to what Tom wrote, you have to use the ‘open’ command to create a series, you can’t use the open-file dialog.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
I'm really a novice to chimerax, so please forgive me to ask two more questions... I have created a volume morph by 'volume morph #1-10', and after that, * How to open a morph control window (with a slider bar, play/stop/... buttons, etc.) * How to create a movie file from the morph (a single run of the morph) It is difficult for me to find out how in the document https://www.rbvi.ucsf.edu/chimerax/docs/user/movies.html Thank you Kotaro On 2020/06/09 0:41, Eric Pettersen wrote:
On Jun 8, 2020, at 6:35 AM, Kotaro TANAKA <kttn8769@gmail.com <mailto:kttn8769@gmail.com>> wrote:
I should obtain a volume series simply by opening the maps at once in a file opening dialogue.
To follow up to what Tom wrote, you have to use the ‘open’ command to create a series, you can’t use the open-file dialog.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
Hi Kotaro, My understanding is that: (1) a volume morph is different than a volume series, and there is no option to show a slider control for a volume morph (2) "volume morph" is the command to show the volume morphing (3) you can record it by putting a "movie record" command before the "volume morph" command, and a "movie encode" command after it. For example, you could put commands something like the following in a plain-text file named myscript.cxc, and then open myscript.cxc in ChimeraX to execute it: movie record volume morph #1-10 playStep 0.01 frames 100; wait 100 movie stop movie encode mymovie.mp4 See explanation of options of the "volume morph" command: <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> Options of the "movie" command: <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/movie.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 8, 2020, at 6:08 PM, Kotaro TANAKA <kttn8769@gmail.com> wrote:
I'm really a novice to chimerax, so please forgive me to ask two more questions...
I have created a volume morph by 'volume morph #1-10', and after that,
* How to open a morph control window (with a slider bar, play/stop/... buttons, etc.) * How to create a movie file from the morph (a single run of the morph)
It is difficult for me to find out how in the document https://www.rbvi.ucsf.edu/chimerax/docs/user/movies.html
Thank you
Kotaro
Hi Kotaro, Unfortunately ChimeraX does not yet have a slider for playing through the morph. There is a feature request for this https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2784 You can replay the morph without creating a new copy of it by specifying the id number of the morph volume morph #1-10 model #11 To record a movie movie record ; volume morph #1-10 model #11 ; wait 250 ; movie encode ~/Desktop/mapmorph.mp4 Commands are separated by semicolors. The volume morph command shows 25 frames per step by default but it returns immediately, so the "wait 250" command says to wait that many frames before going to the next command which outputs the movie file. Our older program Chimera has a user interface panel with a slider and a Record button so it a bit easier to use currently. But it doesn't have nice ambient shadow lighting ("light soft"). In the future we will have a morph user interface panel in ChimeraX. Tom
On Jun 8, 2020, at 6:08 PM, Kotaro TANAKA <kttn8769@gmail.com> wrote:
I'm really a novice to chimerax, so please forgive me to ask two more questions...
I have created a volume morph by 'volume morph #1-10', and after that,
* How to open a morph control window (with a slider bar, play/stop/... buttons, etc.) * How to create a movie file from the morph (a single run of the morph)
It is difficult for me to find out how in the document https://www.rbvi.ucsf.edu/chimerax/docs/user/movies.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/movies.html> Thank you
Kotaro
On 2020/06/09 0:41, Eric Pettersen wrote:
On Jun 8, 2020, at 6:35 AM, Kotaro TANAKA <kttn8769@gmail.com <mailto:kttn8769@gmail.com>> wrote:
I should obtain a volume series simply by opening the maps at once in a file opening dialogue.
To follow up to what Tom wrote, you have to use the ‘open’ command to create a series, you can’t use the open-file dialog.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine and Tom, Thank you for your comments! Now I have obtained my desired movie. Kotaro On 2020/06/09 10:36, Tom Goddard wrote:
Hi Kotaro,
Unfortunately ChimeraX does not yet have a slider for playing through the morph. There is a feature request for this
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2784
You can replay the morph without creating a new copy of it by specifying the id number of the morph
volume morph #1-10 model #11
To record a movie
movie record ; volume morph #1-10 model #11 ; wait 250 ; movie encode ~/Desktop/mapmorph.mp4
Commands are separated by semicolors. The volume morph command shows 25 frames per step by default but it returns immediately, so the "wait 250" command says to wait that many frames before going to the next command which outputs the movie file.
Our older program Chimera has a user interface panel with a slider and a Record button so it a bit easier to use currently. But it doesn't have nice ambient shadow lighting ("light soft"). In the future we will have a morph user interface panel in ChimeraX.
Tom
On Jun 8, 2020, at 6:08 PM, Kotaro TANAKA <kttn8769@gmail.com <mailto:kttn8769@gmail.com>> wrote:
I'm really a novice to chimerax, so please forgive me to ask two more questions...
I have created a volume morph by 'volume morph #1-10', and after that,
* How to open a morph control window (with a slider bar, play/stop/... buttons, etc.) * How to create a movie file from the morph (a single run of the morph)
It is difficult for me to find out how in the document https://www.rbvi.ucsf.edu/chimerax/docs/user/movies.html
Thank you
Kotaro
On 2020/06/09 0:41, Eric Pettersen wrote:
On Jun 8, 2020, at 6:35 AM, Kotaro TANAKA <kttn8769@gmail.com <mailto:kttn8769@gmail.com>> wrote:
I should obtain a volume series simply by opening the maps at once in a file opening dialogue.
To follow up to what Tom wrote, you have to use the ‘open’ command to create a series, you can’t use the open-file dialog.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Elaine Meng -
Eric Pettersen -
Kotaro TANAKA -
Tom Goddard