Combining two volumes
Tatiana writes: Dear ChimeraX developers, I would like your help to combine two volumes in ChimeraX while keeping the properties of each volume (colour, threshold...). I know it's borderline in ChimeraX, but it seems feasible. I have been playing with morph, vop commands and a lot of information found on the web for several days, but I fail. I'm also asking chapGPT... but I can't manage to combine my two volumes. Could you please help me to combine these two attached volumes. If yes, could you please send me the procedure And one more questions related to this question, How to know the name of the slider after vop morph command to synchronise 2 morph and record a movie. I found a way to do it on the web (via the Tools menu and selecting General Controls to open the General Controls panel. In the General Controls panel you will find various sliders) but I don't have this General Controls menu in ChimeraX. Thank you very much if you have time to help me. Tatiana
Hi Tatiana, I'm not sure what you are trying to do. If you combine two maps, for instance, with the "volume add" command you will get a single map, and you can show its surface at a single threshold and in a single color. So I'm not sure what you mean by "keeping the properties of each". Is your purpose to make a movie? I don't see a reason to combine maps to make a movie. Also I don't understand why you want the name of the slider for a volume morph. To play two morphs at the same time in ChimeraX you would use a command script like movie record volume morph #1,2 volume morph #3,4 wait 25 movie encode mymovie.mp4 Both morphs will play at the same time. The first morph command returns immediately just says to start playing the morph. So both morphs start playing at the next rendered graphics frame which happens when you say "wait 25" which means render 25 frames. If you wanted to play the first morph, and after that the second morph and record a movie the commands would be movie record volume morph #1,2 wait 25 volume morph #3,4 wait 25 movie encode mymovie.mp4 with the "wait 25" command after each morph. Tom
On Jun 21, 2023, at 11:30 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Tatiana writes:
Dear ChimeraX developers,
I would like your help to combine two volumes in ChimeraX while keeping the properties of each volume (colour, threshold...). I know it's borderline in ChimeraX, but it seems feasible. I have been playing with morph, vop commands and a lot of information found on the web for several days, but I fail. I'm also asking chapGPT... but I can't manage to combine my two volumes. Could you please help me to combine these two attached volumes. If yes, could you please send me the procedure
And one more questions related to this question, How to know the name of the slider after vop morph command to synchronise 2 morph and record a movie. I found a way to do it on the web (via the Tools menu and selecting General Controls to open the General Controls panel. In the General Controls panel you will find various sliders) but I don't have this General Controls menu in ChimeraX.
Thank you very much if you have time to help me.
Tatiana _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi tom, Thank you a lot for your help. It did not completely work. Applying your first script create a movie with the 2 morphs sequentially displayed. To complete our case, adding these two volumes doesn't work and provide a weird discrete histogram (4 histogram blocks). The volume are gaussian filtered hdf files. And as you said, we don't want the same color for both maps in the movie. A cumbersome way to do it is to move the two sliders at the same image position (160 images in total) at each frame together and take a snapshot and combine these snapshots in a movie using FIJI. That's why we wanted to synchronize both morph sliders while recording the final movie. But we don't have the name of both sliders so we can not script the recording and the movie. Is there a way to find the names of the sliders for both morphs? Thanks in advance for your help Best wishes Tatiana ----- Mail original ----- De: "Tom Goddard" <goddard@sonic.net> À: "ISABET Tatiana" <tatiana.isabet@synchrotron-soleil.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Mercredi 21 Juin 2023 20:47:46 Objet: Re: [chimerax-users] Combining two volumes Hi Tatiana, I'm not sure what you are trying to do. If you combine two maps, for instance, with the "volume add" command you will get a single map, and you can show its surface at a single threshold and in a single color. So I'm not sure what you mean by "keeping the properties of each". Is your purpose to make a movie? I don't see a reason to combine maps to make a movie. Also I don't understand why you want the name of the slider for a volume morph. To play two morphs at the same time in ChimeraX you would use a command script like movie record volume morph #1,2 volume morph #3,4 wait 25 movie encode mymovie.mp4 Both morphs will play at the same time. The first morph command returns immediately just says to start playing the morph. So both morphs start playing at the next rendered graphics frame which happens when you say "wait 25" which means render 25 frames. If you wanted to play the first morph, and after that the second morph and record a movie the commands would be movie record volume morph #1,2 wait 25 volume morph #3,4 wait 25 movie encode mymovie.mp4 with the "wait 25" command after each morph. Tom
On Jun 21, 2023, at 11:30 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Tatiana writes:
Dear ChimeraX developers,
I would like your help to combine two volumes in ChimeraX while keeping the properties of each volume (colour, threshold...). I know it's borderline in ChimeraX, but it seems feasible. I have been playing with morph, vop commands and a lot of information found on the web for several days, but I fail. I'm also asking chapGPT... but I can't manage to combine my two volumes. Could you please help me to combine these two attached volumes. If yes, could you please send me the procedure
And one more questions related to this question, How to know the name of the slider after vop morph command to synchronise 2 morph and record a movie. I found a way to do it on the web (via the Tools menu and selecting General Controls to open the General Controls panel. In the General Controls panel you will find various sliders) but I don't have this General Controls menu in ChimeraX.
Thank you very much if you have time to help me.
Tatiana _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi Tatiana, When you record a movie you don't type those commands into the command-line. If you do that the first morph will finish before you have time to type the second morph command. Instead you put them in a command file mymovie.cxc and open that in ChimeraX (open mymovie.cxc). Alternatively you can put all the commands on the command-line separated by semicolons. Here's an example open 27346 27347 27349 27350 from emdb move x 300 model #3,4 view all movie record ; volume morph #1,2 ; volume morph #3,4 ; wait 25 ; movie encode simultaneous.mp4 Remote controlling sliders or combining the maps into a single map is a very hard way to make a movie. Tom
On Jun 22, 2023, at 6:48 AM, ISABET Tatiana via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi tom,
Thank you a lot for your help. It did not completely work. Applying your first script create a movie with the 2 morphs sequentially displayed. To complete our case, adding these two volumes doesn't work and provide a weird discrete histogram (4 histogram blocks). The volume are gaussian filtered hdf files. And as you said, we don't want the same color for both maps in the movie.
A cumbersome way to do it is to move the two sliders at the same image position (160 images in total) at each frame together and take a snapshot and combine these snapshots in a movie using FIJI. That's why we wanted to synchronize both morph sliders while recording the final movie. But we don't have the name of both sliders so we can not script the recording and the movie. Is there a way to find the names of the sliders for both morphs?
Thanks in advance for your help
Best wishes
Tatiana
----- Mail original ----- De: "Tom Goddard" <goddard@sonic.net> À: "ISABET Tatiana" <tatiana.isabet@synchrotron-soleil.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Mercredi 21 Juin 2023 20:47:46 Objet: Re: [chimerax-users] Combining two volumes
Hi Tatiana,
I'm not sure what you are trying to do. If you combine two maps, for instance, with the "volume add" command you will get a single map, and you can show its surface at a single threshold and in a single color. So I'm not sure what you mean by "keeping the properties of each". Is your purpose to make a movie? I don't see a reason to combine maps to make a movie. Also I don't understand why you want the name of the slider for a volume morph. To play two morphs at the same time in ChimeraX you would use a command script like
movie record volume morph #1,2 volume morph #3,4 wait 25 movie encode mymovie.mp4
Both morphs will play at the same time. The first morph command returns immediately just says to start playing the morph. So both morphs start playing at the next rendered graphics frame which happens when you say "wait 25" which means render 25 frames. If you wanted to play the first morph, and after that the second morph and record a movie the commands would be
movie record volume morph #1,2 wait 25 volume morph #3,4 wait 25 movie encode mymovie.mp4
with the "wait 25" command after each morph.
Tom
On Jun 21, 2023, at 11:30 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Tatiana writes:
Dear ChimeraX developers,
I would like your help to combine two volumes in ChimeraX while keeping the properties of each volume (colour, threshold...). I know it's borderline in ChimeraX, but it seems feasible. I have been playing with morph, vop commands and a lot of information found on the web for several days, but I fail. I'm also asking chapGPT... but I can't manage to combine my two volumes. Could you please help me to combine these two attached volumes. If yes, could you please send me the procedure
And one more questions related to this question, How to know the name of the slider after vop morph command to synchronise 2 morph and record a movie. I found a way to do it on the web (via the Tools menu and selecting General Controls to open the General Controls panel. In the General Controls panel you will find various sliders) but I don't have this General Controls menu in ChimeraX.
Thank you very much if you have time to help me.
Tatiana _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi Tatiana, See the User Guide "making movies" page: <https://rbvi.ucsf.edu/chimerax/docs/user/movies.html> It includes links to tutorials and other pages that have example movie scripts (ChimeraX command files). ChimeraX command files are also described at the bottom of this page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...> 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 22, 2023, at 1:13 PM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Tatiana,
When you record a movie you don't type those commands into the command-line. If you do that the first morph will finish before you have time to type the second morph command. Instead you put them in a command file mymovie.cxc and open that in ChimeraX (open mymovie.cxc). Alternatively you can put all the commands on the command-line separated by semicolons. Here's an example
open 27346 27347 27349 27350 from emdb move x 300 model #3,4 view all
movie record ; volume morph #1,2 ; volume morph #3,4 ; wait 25 ; movie encode simultaneous.mp4
Remote controlling sliders or combining the maps into a single map is a very hard way to make a movie.
Tom
On Jun 22, 2023, at 6:48 AM, ISABET Tatiana via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi tom,
Thank you a lot for your help. It did not completely work. Applying your first script create a movie with the 2 morphs sequentially displayed. To complete our case, adding these two volumes doesn't work and provide a weird discrete histogram (4 histogram blocks). The volume are gaussian filtered hdf files. And as you said, we don't want the same color for both maps in the movie.
A cumbersome way to do it is to move the two sliders at the same image position (160 images in total) at each frame together and take a snapshot and combine these snapshots in a movie using FIJI. That's why we wanted to synchronize both morph sliders while recording the final movie. But we don't have the name of both sliders so we can not script the recording and the movie. Is there a way to find the names of the sliders for both morphs?
Thanks in advance for your help
Best wishes
Tatiana
----- Mail original ----- De: "Tom Goddard" <goddard@sonic.net> À: "ISABET Tatiana" <tatiana.isabet@synchrotron-soleil.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Mercredi 21 Juin 2023 20:47:46 Objet: Re: [chimerax-users] Combining two volumes
Hi Tatiana,
I'm not sure what you are trying to do. If you combine two maps, for instance, with the "volume add" command you will get a single map, and you can show its surface at a single threshold and in a single color. So I'm not sure what you mean by "keeping the properties of each". Is your purpose to make a movie? I don't see a reason to combine maps to make a movie. Also I don't understand why you want the name of the slider for a volume morph. To play two morphs at the same time in ChimeraX you would use a command script like
movie record volume morph #1,2 volume morph #3,4 wait 25 movie encode mymovie.mp4
Both morphs will play at the same time. The first morph command returns immediately just says to start playing the morph. So both morphs start playing at the next rendered graphics frame which happens when you say "wait 25" which means render 25 frames. If you wanted to play the first morph, and after that the second morph and record a movie the commands would be
movie record volume morph #1,2 wait 25 volume morph #3,4 wait 25 movie encode mymovie.mp4
with the "wait 25" command after each morph.
Tom
On Jun 21, 2023, at 11:30 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Tatiana writes:
Dear ChimeraX developers,
I would like your help to combine two volumes in ChimeraX while keeping the properties of each volume (colour, threshold...). I know it's borderline in ChimeraX, but it seems feasible. I have been playing with morph, vop commands and a lot of information found on the web for several days, but I fail. I'm also asking chapGPT... but I can't manage to combine my two volumes. Could you please help me to combine these two attached volumes. If yes, could you please send me the procedure
And one more questions related to this question, How to know the name of the slider after vop morph command to synchronise 2 morph and record a movie. I found a way to do it on the web (via the Tools menu and selecting General Controls to open the General Controls panel. In the General Controls panel you will find various sliders) but I don't have this General Controls menu in ChimeraX.
Thank you very much if you have time to help me.
Tatiana _______________________________________________
Hi Tom, Thank you very much for your help. I did manage to make the movie thanks to your help. One very last question, being able to synchronize the sliders of the two morphs would be very useful to analyse the data before making the movie. Would it be possible to synchronize them (not to make the movie you told that it's not the best way to do. But just to analyse the data)? Maybe getting the name of the sliders to use the synchronize_sliders function for example? Anyway thank you a lot for your help. That was key for the progress of the project. Tatiana ----- Mail original ----- De: "Tom Goddard" <goddard@sonic.net> À: "ISABET Tatiana" <tatiana.isabet@synchrotron-soleil.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Jeudi 22 Juin 2023 22:13:00 Objet: Re: [chimerax-users] Combining two volumes Hi Tatiana, When you record a movie you don't type those commands into the command-line. If you do that the first morph will finish before you have time to type the second morph command. Instead you put them in a command file mymovie.cxc and open that in ChimeraX (open mymovie.cxc). Alternatively you can put all the commands on the command-line separated by semicolons. Here's an example open 27346 27347 27349 27350 from emdb move x 300 model #3,4 view all movie record ; volume morph #1,2 ; volume morph #3,4 ; wait 25 ; movie encode simultaneous.mp4 Remote controlling sliders or combining the maps into a single map is a very hard way to make a movie. Tom
On Jun 22, 2023, at 6:48 AM, ISABET Tatiana via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi tom,
Thank you a lot for your help. It did not completely work. Applying your first script create a movie with the 2 morphs sequentially displayed. To complete our case, adding these two volumes doesn't work and provide a weird discrete histogram (4 histogram blocks). The volume are gaussian filtered hdf files. And as you said, we don't want the same color for both maps in the movie.
A cumbersome way to do it is to move the two sliders at the same image position (160 images in total) at each frame together and take a snapshot and combine these snapshots in a movie using FIJI. That's why we wanted to synchronize both morph sliders while recording the final movie. But we don't have the name of both sliders so we can not script the recording and the movie. Is there a way to find the names of the sliders for both morphs?
Thanks in advance for your help
Best wishes
Tatiana
----- Mail original ----- De: "Tom Goddard" <goddard@sonic.net> À: "ISABET Tatiana" <tatiana.isabet@synchrotron-soleil.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Mercredi 21 Juin 2023 20:47:46 Objet: Re: [chimerax-users] Combining two volumes
Hi Tatiana,
I'm not sure what you are trying to do. If you combine two maps, for instance, with the "volume add" command you will get a single map, and you can show its surface at a single threshold and in a single color. So I'm not sure what you mean by "keeping the properties of each". Is your purpose to make a movie? I don't see a reason to combine maps to make a movie. Also I don't understand why you want the name of the slider for a volume morph. To play two morphs at the same time in ChimeraX you would use a command script like
movie record volume morph #1,2 volume morph #3,4 wait 25 movie encode mymovie.mp4
Both morphs will play at the same time. The first morph command returns immediately just says to start playing the morph. So both morphs start playing at the next rendered graphics frame which happens when you say "wait 25" which means render 25 frames. If you wanted to play the first morph, and after that the second morph and record a movie the commands would be
movie record volume morph #1,2 wait 25 volume morph #3,4 wait 25 movie encode mymovie.mp4
with the "wait 25" command after each morph.
Tom
On Jun 21, 2023, at 11:30 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Tatiana writes:
Dear ChimeraX developers,
I would like your help to combine two volumes in ChimeraX while keeping the properties of each volume (colour, threshold...). I know it's borderline in ChimeraX, but it seems feasible. I have been playing with morph, vop commands and a lot of information found on the web for several days, but I fail. I'm also asking chapGPT... but I can't manage to combine my two volumes. Could you please help me to combine these two attached volumes. If yes, could you please send me the procedure
And one more questions related to this question, How to know the name of the slider after vop morph command to synchronise 2 morph and record a movie. I found a way to do it on the web (via the Tools menu and selecting General Controls to open the General Controls panel. In the General Controls panel you will find various sliders) but I don't have this General Controls menu in ChimeraX.
Thank you very much if you have time to help me.
Tatiana _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
Hi Tatiana, I don't know what you mean by the "synchronize_sliders" function. There is nothing to synchronize sliders in ChimeraX. Also don't know what you mean by the "name" of the sliders. Tom
On Jun 28, 2023, at 1:12 AM, ISABET Tatiana <tatiana.isabet@synchrotron-soleil.fr> wrote:
Hi Tom,
Thank you very much for your help. I did manage to make the movie thanks to your help.
One very last question, being able to synchronize the sliders of the two morphs would be very useful to analyse the data before making the movie. Would it be possible to synchronize them (not to make the movie you told that it's not the best way to do. But just to analyse the data)? Maybe getting the name of the sliders to use the synchronize_sliders function for example?
Anyway thank you a lot for your help. That was key for the progress of the project.
Tatiana
----- Mail original ----- De: "Tom Goddard" <goddard@sonic.net> À: "ISABET Tatiana" <tatiana.isabet@synchrotron-soleil.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Jeudi 22 Juin 2023 22:13:00 Objet: Re: [chimerax-users] Combining two volumes
Hi Tatiana,
When you record a movie you don't type those commands into the command-line. If you do that the first morph will finish before you have time to type the second morph command. Instead you put them in a command file mymovie.cxc and open that in ChimeraX (open mymovie.cxc). Alternatively you can put all the commands on the command-line separated by semicolons. Here's an example
open 27346 27347 27349 27350 from emdb move x 300 model #3,4 view all
movie record ; volume morph #1,2 ; volume morph #3,4 ; wait 25 ; movie encode simultaneous.mp4
Remote controlling sliders or combining the maps into a single map is a very hard way to make a movie.
Tom
On Jun 22, 2023, at 6:48 AM, ISABET Tatiana via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi tom,
Thank you a lot for your help. It did not completely work. Applying your first script create a movie with the 2 morphs sequentially displayed. To complete our case, adding these two volumes doesn't work and provide a weird discrete histogram (4 histogram blocks). The volume are gaussian filtered hdf files. And as you said, we don't want the same color for both maps in the movie.
A cumbersome way to do it is to move the two sliders at the same image position (160 images in total) at each frame together and take a snapshot and combine these snapshots in a movie using FIJI. That's why we wanted to synchronize both morph sliders while recording the final movie. But we don't have the name of both sliders so we can not script the recording and the movie. Is there a way to find the names of the sliders for both morphs?
Thanks in advance for your help
Best wishes
Tatiana
----- Mail original ----- De: "Tom Goddard" <goddard@sonic.net> À: "ISABET Tatiana" <tatiana.isabet@synchrotron-soleil.fr> Cc: "ChimeraX Users Help" <chimerax-users@cgl.ucsf.edu> Envoyé: Mercredi 21 Juin 2023 20:47:46 Objet: Re: [chimerax-users] Combining two volumes
Hi Tatiana,
I'm not sure what you are trying to do. If you combine two maps, for instance, with the "volume add" command you will get a single map, and you can show its surface at a single threshold and in a single color. So I'm not sure what you mean by "keeping the properties of each". Is your purpose to make a movie? I don't see a reason to combine maps to make a movie. Also I don't understand why you want the name of the slider for a volume morph. To play two morphs at the same time in ChimeraX you would use a command script like
movie record volume morph #1,2 volume morph #3,4 wait 25 movie encode mymovie.mp4
Both morphs will play at the same time. The first morph command returns immediately just says to start playing the morph. So both morphs start playing at the next rendered graphics frame which happens when you say "wait 25" which means render 25 frames. If you wanted to play the first morph, and after that the second morph and record a movie the commands would be
movie record volume morph #1,2 wait 25 volume morph #3,4 wait 25 movie encode mymovie.mp4
with the "wait 25" command after each morph.
Tom
On Jun 21, 2023, at 11:30 AM, Tom Goddard via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Tatiana writes:
Dear ChimeraX developers,
I would like your help to combine two volumes in ChimeraX while keeping the properties of each volume (colour, threshold...). I know it's borderline in ChimeraX, but it seems feasible. I have been playing with morph, vop commands and a lot of information found on the web for several days, but I fail. I'm also asking chapGPT... but I can't manage to combine my two volumes. Could you please help me to combine these two attached volumes. If yes, could you please send me the procedure
And one more questions related to this question, How to know the name of the slider after vop morph command to synchronise 2 morph and record a movie. I found a way to do it on the web (via the Tools menu and selecting General Controls to open the General Controls panel. In the General Controls panel you will find various sliders) but I don't have this General Controls menu in ChimeraX.
Thank you very much if you have time to help me.
Tatiana _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
_______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Manage subscription:
participants (3)
-
Elaine Meng -
ISABET Tatiana -
Tom Goddard