Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result? Thank you so much for any help -- *Henrique C. S. Junior* Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <http://mundoquimico.com.br>
Is there a command to show/hide surfaces that does the same as checking/unchecking the GUI model panel hide box?. Or something equivalent to the comands: ~show ribbon ~ribbon for atoms and ribbons ? Thks H.
Hi Hernando, To hide and show the whole model without changing individual atom/ribbon display (same as checking the Model Panel “S” box), use the “modeldisplay” command, for example: ~modeldisp #4 modeldisp #2-5 see <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/modeldisplay.html> It also works with surface models, but since a molecular surface generally has the same model number as the atomic model it was based on, it is tricky to specify it separately. Here is a somewhat ugly example of specifying only surface model #0 but not atomic model #0: ~modeldisp #0 & ~ @* (hide model 0 but not any atoms). If you just used #0 it would hide both atomic model #0 and surface model #0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2017, at 3:51 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Is there a command to show/hide surfaces that does the same as checking/unchecking the GUI model panel hide box?. Or something equivalent to the comands: ~show ribbon ~ribbon for atoms and ribbons ? Thks H.
Thanks Elaine, That would work -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Wednesday, October 11, 2017 7:49 PM To: Hernando J Sosa Cc: Chimera User Forum Subject: Re: [Chimera-users] show/hide surface Hi Hernando, To hide and show the whole model without changing individual atom/ribbon display (same as checking the Model Panel “S” box), use the “modeldisplay” command, for example: ~modeldisp #4 modeldisp #2-5 see <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/modeldisplay.html> It also works with surface models, but since a molecular surface generally has the same model number as the atomic model it was based on, it is tricky to specify it separately. Here is a somewhat ugly example of specifying only surface model #0 but not atomic model #0: ~modeldisp #0 & ~ @* (hide model 0 but not any atoms). If you just used #0 it would hide both atomic model #0 and surface model #0. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2017, at 3:51 PM, Hernando J Sosa <hernando.sosa@einstein.yu.edu> wrote:
Is there a command to show/hide surfaces that does the same as checking/unchecking the GUI model panel hide box?. Or something equivalent to the comands: ~show ribbon ~ribbon for atoms and ribbons ? Thks H.
Dear Henrique, There is a “Volume Series” graphical tool (or “vseries” command) to open a series of map files and show them in order: The tool is in the menu under Tools… Volume Data. The map files would need to be named so that they open in the right order. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volseries/volserie...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vseries.html> To record a movie file, you would need to make a Chimera command script including the “vseries” command to play back the frames of your volume series, “movie” to record and save the movie, and any other things you might want in your movie (coloring, labels, motions, …) Movie-related commands and example command files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2017, at 3:42 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result?
Thank you so much for any help -- Henrique C. S. Junior Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico
Dear Elaine, thank you, you're amazing. I'm using Chimera 1.12 (Build 41600) and following your instructions, it looks like Chimera is importing the same .cube over and over again. (can you see the little video attached?) On Wed, Oct 11, 2017 at 9:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Henrique, There is a “Volume Series” graphical tool (or “vseries” command) to open a series of map files and show them in order:
The tool is in the menu under Tools… Volume Data. The map files would need to be named so that they open in the right order. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volseries/ volseries.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vseries.html>
To record a movie file, you would need to make a Chimera command script including the “vseries” command to play back the frames of your volume series, “movie” to record and save the movie, and any other things you might want in your movie (coloring, labels, motions, …)
Movie-related commands and example command files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/ movies.html#moviecommands>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2017, at 3:42 PM, Henrique C. S. Junior < henriquecsj@gmail.com> wrote:
Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result?
Thank you so much for any help -- Henrique C. S. Junior Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico
-- *Henrique C. S. Junior* Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <http://mundoquimico.com.br>
Hi Henrique, Sorry, I can’t view the movie. If you could give an example of how your files are named (like the names of the first few) and how you are opening them, we may understand better: If using a dialog, how did you get the dialog and what did you choose in the dialog, or if using a command to open, what was the command? If you want us to try your data, you could send a small sample, like your first 3-5 files to just me (meng@cgl.ucsf.edu). Thanks, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2017, at 8:09 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
Dear Elaine, thank you, you're amazing. I'm using Chimera 1.12 (Build 41600) and following your instructions, it looks like Chimera is importing the same .cube over and over again. (can you see the little video attached?)
On Wed, Oct 11, 2017 at 9:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Henrique, There is a “Volume Series” graphical tool (or “vseries” command) to open a series of map files and show them in order:
The tool is in the menu under Tools… Volume Data. The map files would need to be named so that they open in the right order. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volseries/volserie...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vseries.html>
To record a movie file, you would need to make a Chimera command script including the “vseries” command to play back the frames of your volume series, “movie” to record and save the movie, and any other things you might want in your movie (coloring, labels, motions, …)
Movie-related commands and example command files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
I hope this helps, Elaine
On Oct 11, 2017, at 3:42 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result?
Thank you so much for any help
Sorry, Elaine, here are some screenshots to clarify (attached). The .cube files are all sequentially numbered (but not at the beginning of the name). On Thu, Oct 12, 2017 at 2:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Henrique, Sorry, I can’t view the movie.
If you could give an example of how your files are named (like the names of the first few) and how you are opening them, we may understand better: If using a dialog, how did you get the dialog and what did you choose in the dialog, or if using a command to open, what was the command?
If you want us to try your data, you could send a small sample, like your first 3-5 files to just me (meng@cgl.ucsf.edu). Thanks, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Oct 11, 2017, at 8:09 PM, Henrique C. S. Junior < henriquecsj@gmail.com> wrote:
Dear Elaine, thank you, you're amazing. I'm using Chimera 1.12 (Build 41600) and following your instructions, it looks like Chimera is importing the same .cube over and over again. (can you see the little video attached?)
On Wed, Oct 11, 2017 at 9:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Henrique, There is a “Volume Series” graphical tool (or “vseries” command) to open a series of map files and show them in order:
The tool is in the menu under Tools… Volume Data. The map files would need to be named so that they open in the right order. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volseries/ volseries.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vseries.html>
To record a movie file, you would need to make a Chimera command script including the “vseries” command to play back the frames of your volume series, “movie” to record and save the movie, and any other things you might want in your movie (coloring, labels, motions, …)
Movie-related commands and example command files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/ movies.html#moviecommands>
I hope this helps, Elaine
On Oct 11, 2017, at 3:42 PM, Henrique C. S. Junior < henriquecsj@gmail.com> wrote:
Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result?
Thank you so much for any help
-- *Henrique C. S. Junior* Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <http://mundoquimico.com.br>
Hi Henrique, I must admit I have no idea how to show that “Volume Memory Manager” dialog in one of your images… I’ve ever seen it before!!! However, it might be that things are working correctly, but the same name shown for each dataset because it is part of a series ( and the name of the series comes from the name of the first file). Without having a few of your files to test with, I can’t tell if they are causing some problem. If you ignore the names shown in that dialog, is there any other reason to think it's not working? When you play across time using the Volume Series dialog, does the isosurface change like you expect, or does it stay exactly the same? If things are too slow opening ALL of your files, you could try opening a smaller subset of them for testing purposes. Elaine
On Oct 12, 2017, at 1:47 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
Sorry, Elaine, here are some screenshots to clarify (attached). The .cube files are all sequentially numbered (but not at the beginning of the name).
On Thu, Oct 12, 2017 at 2:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Henrique, Sorry, I can’t view the movie.
If you could give an example of how your files are named (like the names of the first few) and how you are opening them, we may understand better: If using a dialog, how did you get the dialog and what did you choose in the dialog, or if using a command to open, what was the command?
If you want us to try your data, you could send a small sample, like your first 3-5 files to just me (meng@cgl.ucsf.edu). Thanks, Elaine
On Oct 11, 2017, at 8:09 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
Dear Elaine, thank you, you're amazing. I'm using Chimera 1.12 (Build 41600) and following your instructions, it looks like Chimera is importing the same .cube over and over again. (can you see the little video attached?)
On Wed, Oct 11, 2017 at 9:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Henrique, There is a “Volume Series” graphical tool (or “vseries” command) to open a series of map files and show them in order:
The tool is in the menu under Tools… Volume Data. The map files would need to be named so that they open in the right order. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volseries/volserie...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vseries.html>
To record a movie file, you would need to make a Chimera command script including the “vseries” command to play back the frames of your volume series, “movie” to record and save the movie, and any other things you might want in your movie (coloring, labels, motions, …)
Movie-related commands and example command files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
I hope this helps, Elaine
On Oct 11, 2017, at 3:42 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result?
Thank you so much for any help
-- Henrique C. S. Junior Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <2017-10-12 (1).png><2017-10-12 (7).png><2017-10-12 (6).png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
The volume is always the same, Elaine. I have renamed all my files to something more simple, like 001.cube (to 500.cube) and only the first frame is loaded. If I click PLAY it looks like it is changing frames, it flicks only to the first frame forever. Volume viewer shows only one surface loaded, by the way. Is it of any help if I could provide some .cube files to test? Because it looks like a bug, don't you think? On Thu, Oct 12, 2017 at 7:45 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Henrique, I must admit I have no idea how to show that “Volume Memory Manager” dialog in one of your images… I’ve ever seen it before!!!
However, it might be that things are working correctly, but the same name shown for each dataset because it is part of a series ( and the name of the series comes from the name of the first file). Without having a few of your files to test with, I can’t tell if they are causing some problem.
If you ignore the names shown in that dialog, is there any other reason to think it's not working? When you play across time using the Volume Series dialog, does the isosurface change like you expect, or does it stay exactly the same?
If things are too slow opening ALL of your files, you could try opening a smaller subset of them for testing purposes.
Elaine
On Oct 12, 2017, at 1:47 PM, Henrique C. S. Junior < henriquecsj@gmail.com> wrote:
Sorry, Elaine, here are some screenshots to clarify (attached). The .cube files are all sequentially numbered (but not at the beginning of the name).
On Thu, Oct 12, 2017 at 2:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Henrique, Sorry, I can’t view the movie.
If you could give an example of how your files are named (like the names of the first few) and how you are opening them, we may understand better: If using a dialog, how did you get the dialog and what did you choose in the dialog, or if using a command to open, what was the command?
If you want us to try your data, you could send a small sample, like your first 3-5 files to just me (meng@cgl.ucsf.edu). Thanks, Elaine
On Oct 11, 2017, at 8:09 PM, Henrique C. S. Junior < henriquecsj@gmail.com> wrote:
Dear Elaine, thank you, you're amazing. I'm using Chimera 1.12 (Build 41600) and following your instructions, it looks like Chimera is importing the same .cube over and over again. (can you see the little video attached?)
On Wed, Oct 11, 2017 at 9:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Henrique, There is a “Volume Series” graphical tool (or “vseries” command) to open a series of map files and show them in order:
The tool is in the menu under Tools… Volume Data. The map files would need to be named so that they open in the right order. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volseries/ volseries.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vseries.html>
To record a movie file, you would need to make a Chimera command script including the “vseries” command to play back the frames of your volume series, “movie” to record and save the movie, and any other things you might want in your movie (coloring, labels, motions, …)
Movie-related commands and example command files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/ movies.html#moviecommands>
I hope this helps, Elaine
On Oct 11, 2017, at 3:42 PM, Henrique C. S. Junior < henriquecsj@gmail.com> wrote:
Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result?
Thank you so much for any help
-- Henrique C. S. Junior Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <2017-10-12 (1).png><2017-10-12 (7).png><2017-10-12 (6).png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/ mailman/listinfo/chimera-users
-- *Henrique C. S. Junior* Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <http://mundoquimico.com.br>
We haven’t seen this problem. If the files are opened as a series, the Volume Viewer will only show one histogram, so that part is expected. However, if the appearance isn’t changing when you play through time with Volume Series and you know your data frames should look different from each other, you could send me a sample, say of the first 10 files. If you zip them into a single file you can use Chimera menu: Help… Report a Bug and attach that zip file to your report. You’d have to put your email address into the bugreport form so that it would be automatically connected to you. You can doublecheck if two frames (data in different cube files) really look different by opening them individually instead of as a series, for example with File… Open in the Chimera main menu. Elaine
On Oct 12, 2017, at 4:07 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
The volume is always the same, Elaine. I have renamed all my files to something more simple, like 001.cube (to 500.cube) and only the first frame is loaded. If I click PLAY it looks like it is changing frames, it flicks only to the first frame forever. Volume viewer shows only one surface loaded, by the way. Is it of any help if I could provide some .cube files to test? Because it looks like a bug, don't you think?
On Thu, Oct 12, 2017 at 7:45 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Henrique, I must admit I have no idea how to show that “Volume Memory Manager” dialog in one of your images… I’ve ever seen it before!!!
However, it might be that things are working correctly, but the same name shown for each dataset because it is part of a series ( and the name of the series comes from the name of the first file). Without having a few of your files to test with, I can’t tell if they are causing some problem.
If you ignore the names shown in that dialog, is there any other reason to think it's not working? When you play across time using the Volume Series dialog, does the isosurface change like you expect, or does it stay exactly the same?
If things are too slow opening ALL of your files, you could try opening a smaller subset of them for testing purposes.
Elaine
On Oct 12, 2017, at 1:47 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
Sorry, Elaine, here are some screenshots to clarify (attached). The .cube files are all sequentially numbered (but not at the beginning of the name).
On Thu, Oct 12, 2017 at 2:27 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Henrique, Sorry, I can’t view the movie.
If you could give an example of how your files are named (like the names of the first few) and how you are opening them, we may understand better: If using a dialog, how did you get the dialog and what did you choose in the dialog, or if using a command to open, what was the command?
If you want us to try your data, you could send a small sample, like your first 3-5 files to just me (meng@cgl.ucsf.edu). Thanks, Elaine
On Oct 11, 2017, at 8:09 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
Dear Elaine, thank you, you're amazing. I'm using Chimera 1.12 (Build 41600) and following your instructions, it looks like Chimera is importing the same .cube over and over again. (can you see the little video attached?)
On Wed, Oct 11, 2017 at 9:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote: Dear Henrique, There is a “Volume Series” graphical tool (or “vseries” command) to open a series of map files and show them in order:
The tool is in the menu under Tools… Volume Data. The map files would need to be named so that they open in the right order. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volseries/volserie...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vseries.html>
To record a movie file, you would need to make a Chimera command script including the “vseries” command to play back the frames of your volume series, “movie” to record and save the movie, and any other things you might want in your movie (coloring, labels, motions, …)
Movie-related commands and example command files: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
I hope this helps, Elaine
On Oct 11, 2017, at 3:42 PM, Henrique C. S. Junior <henriquecsj@gmail.com> wrote:
Dear list, I'm getting results from an RT-TDDFT calculation that generates several (> 450) .cube files and I'd like to know if we have a nice way to generate an animation. I know that Chimera can generate beautiful images, but can I load each .cube as a frame and animate the result?
Thank you so much for any help
-- Henrique C. S. Junior Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico <2017-10-12 (1).png><2017-10-12 (7).png><2017-10-12 (6).png>_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Henrique C. S. Junior Industrial Chemist - UFRRJ M. Sc. Inorganic Chemistry - UFRRJ Data Processing Center - PMP Visite o Mundo Químico _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Henrique C. S. Junior -
Hernando J Sosa