Dear Chimera users, I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs. I think I should use a metafile in this situation. Something like this: namd(psf/dcd) pam.psf pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number? Thank you in advance, Clara Blanes
Hi Clara Blanes, If your computer hangs when you specify multiple DCD files in the dialog, I don’t think it will make any difference to use a metafile since the underlying process is the same. Secondly, even if you successfully entered the multiple DCD files, there is no provision in the movie-recording dialog opened from the MD Movie tool to only show some fraction of the frames from each unless they are evenly spaced out (every Nth frame across the whole thing). I.e., you couldn’t just show the first 30 frames from each DCD. Although you can specify a range of frames to load, it is only one range per trajectory even if the trajectory includes multiple DCD files. Instead, you could try just opening each DCD one at a time (with its PSF) file, then running a Chimera command script to (a) start recording (command “movie record…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html> (b) play the frames you want in your movie (command “coordset…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> (c) stop recording but do not create the movie file yet (“movie stop”) ...close that trajectory, open next one (PSF + DCD), run script to do (a)-(c) above, repeat until done. Or, if you need the structure from one trajectory to be matched in position to the previous trajectory, don’t close the first one until after you opened the second one and matched it onto the first. Then put all the recorded images together into a single movie file (command “movie encode”). Actually, you can do all kinds of fancy other things before, between, and after playing the trajectories, such as rotating the structure (command “turn”), showing title text (“2dlabels”), adding extra frames where there is no motion (“wait”), etc. See Making Movies, movie-related commands, and example movie command files such as “ball-and-socket motion” which includes playing a morph trajectory with “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.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 May 22, 2019, at 3:10 AM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Dear Chimera users,
I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs.
I think I should use a metafile in this situation. Something like this:
namd(psf/dcd)
pam.psf
pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number?
Thank you in advance, Clara Blanes
Just to comment on the "computer hangs” part: it is a known problem on the mac right now that entering enough coordinate files that the dialog tries to add a scrollbar causes Chimera to hang (it’s a problem with the Tk windowing toolkit). There is a simple workaround: before adding the files, resize the dialog large enough so that it won’t need to add a scrollbar. —Eric Eric Pettersen UCSF Computer Graphics Lab
On May 22, 2019, at 10:30 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Clara Blanes, If your computer hangs when you specify multiple DCD files in the dialog, I don’t think it will make any difference to use a metafile since the underlying process is the same.
Secondly, even if you successfully entered the multiple DCD files, there is no provision in the movie-recording dialog opened from the MD Movie tool to only show some fraction of the frames from each unless they are evenly spaced out (every Nth frame across the whole thing). I.e., you couldn’t just show the first 30 frames from each DCD. Although you can specify a range of frames to load, it is only one range per trajectory even if the trajectory includes multiple DCD files.
Instead, you could try just opening each DCD one at a time (with its PSF) file, then running a Chimera command script to
(a) start recording (command “movie record…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
(b) play the frames you want in your movie (command “coordset…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
(c) stop recording but do not create the movie file yet (“movie stop”)
...close that trajectory, open next one (PSF + DCD), run script to do (a)-(c) above, repeat until done. Or, if you need the structure from one trajectory to be matched in position to the previous trajectory, don’t close the first one until after you opened the second one and matched it onto the first.
Then put all the recorded images together into a single movie file (command “movie encode”). Actually, you can do all kinds of fancy other things before, between, and after playing the trajectories, such as rotating the structure (command “turn”), showing title text (“2dlabels”), adding extra frames where there is no motion (“wait”), etc.
See Making Movies, movie-related commands, and example movie command files such as “ball-and-socket motion” which includes playing a morph trajectory with “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.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 May 22, 2019, at 3:10 AM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Dear Chimera users,
I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs.
I think I should use a metafile in this situation. Something like this:
namd(psf/dcd)
pam.psf
pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number?
Thank you in advance, Clara Blanes
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you very much Elaine. I will try your suggestions. Regarding the problem I am having because my computer hang when I loaded the three dcd files…, thank you Eric for your comments. I cannot resize the dialog window because it hangs just when I click on MD/Ensamble Analisis / MD Movie. Before having these problems, I obtained a window where I could browse and add the psf and dcd files but since I had the problem I obtain a white window saying Get Ensemble Info at the header. Nothing inside and I can’t resize it because the spinning wheel is there and I can’t do anything. I have reinstalled Chimera but I obtain the same white window and the spinning wheel when I try to start the MD Movie interface Thank you again for your help, clara
El 22 may 2019, a las 19:30, Elaine Meng <meng@cgl.ucsf.edu> escribió:
Hi Clara Blanes, If your computer hangs when you specify multiple DCD files in the dialog, I don’t think it will make any difference to use a metafile since the underlying process is the same.
Secondly, even if you successfully entered the multiple DCD files, there is no provision in the movie-recording dialog opened from the MD Movie tool to only show some fraction of the frames from each unless they are evenly spaced out (every Nth frame across the whole thing). I.e., you couldn’t just show the first 30 frames from each DCD. Although you can specify a range of frames to load, it is only one range per trajectory even if the trajectory includes multiple DCD files.
Instead, you could try just opening each DCD one at a time (with its PSF) file, then running a Chimera command script to
(a) start recording (command “movie record…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
(b) play the frames you want in your movie (command “coordset…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
(c) stop recording but do not create the movie file yet (“movie stop”)
...close that trajectory, open next one (PSF + DCD), run script to do (a)-(c) above, repeat until done. Or, if you need the structure from one trajectory to be matched in position to the previous trajectory, don’t close the first one until after you opened the second one and matched it onto the first.
Then put all the recorded images together into a single movie file (command “movie encode”). Actually, you can do all kinds of fancy other things before, between, and after playing the trajectories, such as rotating the structure (command “turn”), showing title text (“2dlabels”), adding extra frames where there is no motion (“wait”), etc.
See Making Movies, movie-related commands, and example movie command files such as “ball-and-socket motion” which includes playing a morph trajectory with “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.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 May 22, 2019, at 3:10 AM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Dear Chimera users,
I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs.
I think I should use a metafile in this situation. Something like this:
namd(psf/dcd)
pam.psf
pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number?
Thank you in advance, Clara Blanes
Ah, okay. So start Chimera and open Preferences (Favorites→Preferences) and change “Category” in the resulting dialog to “Preferences”. The dialog will then be showing you the location of your preferences file (among other things). The simplest thing to do is to quit Chimera and then remove your preferences file. This will cause Chimera to forget all you preferences though, including recently opened files — it will be like you are using Chimera for the first time. Alternatively, you can edit the preferences file. Search for the name of one of your DCD files in the preferences file. It should be in a comma-separated list of files between square brackets ([]). Remove everything between the square brackets (but leave the brackets) and write out the file. You should be able to start the MD Movie dialog and use my resizing advice hopefully. Worst case, just remove the preferences file! ;-) —Eric
On May 22, 2019, at 1:13 PM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Thank you very much Elaine. I will try your suggestions. Regarding the problem I am having because my computer hang when I loaded the three dcd files…, thank you Eric for your comments. I cannot resize the dialog window because it hangs just when I click on MD/Ensamble Analisis / MD Movie. Before having these problems, I obtained a window where I could browse and add the psf and dcd files but since I had the problem I obtain a white window saying Get Ensemble Info at the header. Nothing inside and I can’t resize it because the spinning wheel is there and I can’t do anything. I have reinstalled Chimera but I obtain the same white window and the spinning wheel when I try to start the MD Movie interface
Thank you again for your help, clara
El 22 may 2019, a las 19:30, Elaine Meng <meng@cgl.ucsf.edu> escribió:
Hi Clara Blanes, If your computer hangs when you specify multiple DCD files in the dialog, I don’t think it will make any difference to use a metafile since the underlying process is the same.
Secondly, even if you successfully entered the multiple DCD files, there is no provision in the movie-recording dialog opened from the MD Movie tool to only show some fraction of the frames from each unless they are evenly spaced out (every Nth frame across the whole thing). I.e., you couldn’t just show the first 30 frames from each DCD. Although you can specify a range of frames to load, it is only one range per trajectory even if the trajectory includes multiple DCD files.
Instead, you could try just opening each DCD one at a time (with its PSF) file, then running a Chimera command script to
(a) start recording (command “movie record…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
(b) play the frames you want in your movie (command “coordset…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
(c) stop recording but do not create the movie file yet (“movie stop”)
...close that trajectory, open next one (PSF + DCD), run script to do (a)-(c) above, repeat until done. Or, if you need the structure from one trajectory to be matched in position to the previous trajectory, don’t close the first one until after you opened the second one and matched it onto the first.
Then put all the recorded images together into a single movie file (command “movie encode”). Actually, you can do all kinds of fancy other things before, between, and after playing the trajectories, such as rotating the structure (command “turn”), showing title text (“2dlabels”), adding extra frames where there is no motion (“wait”), etc.
See Making Movies, movie-related commands, and example movie command files such as “ball-and-socket motion” which includes playing a morph trajectory with “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.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 May 22, 2019, at 3:10 AM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Dear Chimera users,
I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs.
I think I should use a metafile in this situation. Something like this:
namd(psf/dcd)
pam.psf
pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number?
Thank you in advance, Clara Blanes
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
THANK YOU Eric. It worked!!!!! :) All the best, clara
El 23 may 2019, a las 0:19, Eric Pettersen <pett@cgl.ucsf.edu> escribió:
Ah, okay. So start Chimera and open Preferences (Favorites→Preferences) and change “Category” in the resulting dialog to “Preferences”. The dialog will then be showing you the location of your preferences file (among other things). The simplest thing to do is to quit Chimera and then remove your preferences file. This will cause Chimera to forget all you preferences though, including recently opened files — it will be like you are using Chimera for the first time.
Alternatively, you can edit the preferences file. Search for the name of one of your DCD files in the preferences file. It should be in a comma-separated list of files between square brackets ([]). Remove everything between the square brackets (but leave the brackets) and write out the file. You should be able to start the MD Movie dialog and use my resizing advice hopefully. Worst case, just remove the preferences file! ;-)
—Eric
On May 22, 2019, at 1:13 PM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Thank you very much Elaine. I will try your suggestions. Regarding the problem I am having because my computer hang when I loaded the three dcd files…, thank you Eric for your comments. I cannot resize the dialog window because it hangs just when I click on MD/Ensamble Analisis / MD Movie. Before having these problems, I obtained a window where I could browse and add the psf and dcd files but since I had the problem I obtain a white window saying Get Ensemble Info at the header. Nothing inside and I can’t resize it because the spinning wheel is there and I can’t do anything. I have reinstalled Chimera but I obtain the same white window and the spinning wheel when I try to start the MD Movie interface
Thank you again for your help, clara
El 22 may 2019, a las 19:30, Elaine Meng <meng@cgl.ucsf.edu> escribió:
Hi Clara Blanes, If your computer hangs when you specify multiple DCD files in the dialog, I don’t think it will make any difference to use a metafile since the underlying process is the same.
Secondly, even if you successfully entered the multiple DCD files, there is no provision in the movie-recording dialog opened from the MD Movie tool to only show some fraction of the frames from each unless they are evenly spaced out (every Nth frame across the whole thing). I.e., you couldn’t just show the first 30 frames from each DCD. Although you can specify a range of frames to load, it is only one range per trajectory even if the trajectory includes multiple DCD files.
Instead, you could try just opening each DCD one at a time (with its PSF) file, then running a Chimera command script to
(a) start recording (command “movie record…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
(b) play the frames you want in your movie (command “coordset…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
(c) stop recording but do not create the movie file yet (“movie stop”)
...close that trajectory, open next one (PSF + DCD), run script to do (a)-(c) above, repeat until done. Or, if you need the structure from one trajectory to be matched in position to the previous trajectory, don’t close the first one until after you opened the second one and matched it onto the first.
Then put all the recorded images together into a single movie file (command “movie encode”). Actually, you can do all kinds of fancy other things before, between, and after playing the trajectories, such as rotating the structure (command “turn”), showing title text (“2dlabels”), adding extra frames where there is no motion (“wait”), etc.
See Making Movies, movie-related commands, and example movie command files such as “ball-and-socket motion” which includes playing a morph trajectory with “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.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 May 22, 2019, at 3:10 AM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Dear Chimera users,
I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs.
I think I should use a metafile in this situation. Something like this:
namd(psf/dcd)
pam.psf
pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number?
Thank you in advance, Clara Blanes
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
You’re welcome! Also, I have upgraded Chimera to use the latest version of the Tk windowing toolkit (8.6.9.1), which also seems to fix the problem. The fix will be in tomorrow’s daily build (not the 1.13.1 production release). —Eric
On May 23, 2019, at 12:28 AM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
THANK YOU Eric. It worked!!!!! :)
All the best, clara
El 23 may 2019, a las 0:19, Eric Pettersen <pett@cgl.ucsf.edu> escribió:
Ah, okay. So start Chimera and open Preferences (Favorites→Preferences) and change “Category” in the resulting dialog to “Preferences”. The dialog will then be showing you the location of your preferences file (among other things). The simplest thing to do is to quit Chimera and then remove your preferences file. This will cause Chimera to forget all you preferences though, including recently opened files — it will be like you are using Chimera for the first time.
Alternatively, you can edit the preferences file. Search for the name of one of your DCD files in the preferences file. It should be in a comma-separated list of files between square brackets ([]). Remove everything between the square brackets (but leave the brackets) and write out the file. You should be able to start the MD Movie dialog and use my resizing advice hopefully. Worst case, just remove the preferences file! ;-)
—Eric
On May 22, 2019, at 1:13 PM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Thank you very much Elaine. I will try your suggestions. Regarding the problem I am having because my computer hang when I loaded the three dcd files…, thank you Eric for your comments. I cannot resize the dialog window because it hangs just when I click on MD/Ensamble Analisis / MD Movie. Before having these problems, I obtained a window where I could browse and add the psf and dcd files but since I had the problem I obtain a white window saying Get Ensemble Info at the header. Nothing inside and I can’t resize it because the spinning wheel is there and I can’t do anything. I have reinstalled Chimera but I obtain the same white window and the spinning wheel when I try to start the MD Movie interface
Thank you again for your help, clara
El 22 may 2019, a las 19:30, Elaine Meng <meng@cgl.ucsf.edu> escribió:
Hi Clara Blanes, If your computer hangs when you specify multiple DCD files in the dialog, I don’t think it will make any difference to use a metafile since the underlying process is the same.
Secondly, even if you successfully entered the multiple DCD files, there is no provision in the movie-recording dialog opened from the MD Movie tool to only show some fraction of the frames from each unless they are evenly spaced out (every Nth frame across the whole thing). I.e., you couldn’t just show the first 30 frames from each DCD. Although you can specify a range of frames to load, it is only one range per trajectory even if the trajectory includes multiple DCD files.
Instead, you could try just opening each DCD one at a time (with its PSF) file, then running a Chimera command script to
(a) start recording (command “movie record…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
(b) play the frames you want in your movie (command “coordset…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
(c) stop recording but do not create the movie file yet (“movie stop”)
...close that trajectory, open next one (PSF + DCD), run script to do (a)-(c) above, repeat until done. Or, if you need the structure from one trajectory to be matched in position to the previous trajectory, don’t close the first one until after you opened the second one and matched it onto the first.
Then put all the recorded images together into a single movie file (command “movie encode”). Actually, you can do all kinds of fancy other things before, between, and after playing the trajectories, such as rotating the structure (command “turn”), showing title text (“2dlabels”), adding extra frames where there is no motion (“wait”), etc.
See Making Movies, movie-related commands, and example movie command files such as “ball-and-socket motion” which includes playing a morph trajectory with “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.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 May 22, 2019, at 3:10 AM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Dear Chimera users,
I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs.
I think I should use a metafile in this situation. Something like this:
namd(psf/dcd)
pam.psf
pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number?
Thank you in advance, Clara Blanes
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
For this thread, and anyone else out there who is interested. My student Kyle Diller just published a javascript plug-in for watching and movie making multi-frame PDB files in ChimeraX (note this is not Chimera 1.13) https://cxtoolshed.rbvi.ucsf.edu/apps/moleculardynamicsviewer The main advantage is that it allows use of the VR headset to watch dynamics (via VR on and VR off at command line) For VR, you need to have steamOS with steamVR activated too. With or without VR, it also takes advantage of the new advanced shading available in ChimeraX. Dr Greg A. Babbitt Life Sciences Rochester Institute of Technology ________________________________________ From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> Sent: Wednesday, May 22, 2019 4:13 PM To: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] Recording movie from multiple dcd files Thank you very much Elaine. I will try your suggestions. Regarding the problem I am having because my computer hang when I loaded the three dcd files…, thank you Eric for your comments. I cannot resize the dialog window because it hangs just when I click on MD/Ensamble Analisis / MD Movie. Before having these problems, I obtained a window where I could browse and add the psf and dcd files but since I had the problem I obtain a white window saying Get Ensemble Info at the header. Nothing inside and I can’t resize it because the spinning wheel is there and I can’t do anything. I have reinstalled Chimera but I obtain the same white window and the spinning wheel when I try to start the MD Movie interface Thank you again for your help, clara
El 22 may 2019, a las 19:30, Elaine Meng <meng@cgl.ucsf.edu> escribió:
Hi Clara Blanes, If your computer hangs when you specify multiple DCD files in the dialog, I don’t think it will make any difference to use a metafile since the underlying process is the same.
Secondly, even if you successfully entered the multiple DCD files, there is no provision in the movie-recording dialog opened from the MD Movie tool to only show some fraction of the frames from each unless they are evenly spaced out (every Nth frame across the whole thing). I.e., you couldn’t just show the first 30 frames from each DCD. Although you can specify a range of frames to load, it is only one range per trajectory even if the trajectory includes multiple DCD files.
Instead, you could try just opening each DCD one at a time (with its PSF) file, then running a Chimera command script to
(a) start recording (command “movie record…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
(b) play the frames you want in your movie (command “coordset…”) <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
(c) stop recording but do not create the movie file yet (“movie stop”)
...close that trajectory, open next one (PSF + DCD), run script to do (a)-(c) above, repeat until done. Or, if you need the structure from one trajectory to be matched in position to the previous trajectory, don’t close the first one until after you opened the second one and matched it onto the first.
Then put all the recorded images together into a single movie file (command “movie encode”). Actually, you can do all kinds of fancy other things before, between, and after playing the trajectories, such as rotating the structure (command “turn”), showing title text (“2dlabels”), adding extra frames where there is no motion (“wait”), etc.
See Making Movies, movie-related commands, and example movie command files such as “ball-and-socket motion” which includes playing a morph trajectory with “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.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 May 22, 2019, at 3:10 AM, MARIA CLARA BLANES MIRA <c.blanes@goumh.umh.es> wrote:
Dear Chimera users,
I have a .psf and multiple .dcd files for a peptide movement and I need to make a movie combining certain frames for each dcd file. First, I have tried to load more than one dcd file in the MD movie interface but my computer hungs.
I think I should use a metafile in this situation. Something like this:
namd(psf/dcd)
pam.psf
pam1.dcd But I have all the other pam2.dcd, pam3.dcd, etc until 40, each having 3000 frames. How could I include them in the same metafile to be able to open one, record 20-30 frames, open the second, record some other frames and so on? And how could I include the frames number?
Thank you in advance, Clara Blanes
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Thanks!! By the way, we were very impressed and happy to see this tool appear in the ChimeraX tool shed. Anyone who makes it that far should feel free to announce it on the chimerax-users@cgl.ucsf.edu mailing list. :-) Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 22, 2019, at 3:26 PM, Gregory Babbitt <gabsbi@rit.edu> wrote:
For this thread, and anyone else out there who is interested. My student Kyle Diller just published a javascript plug-in for watching and movie making multi-frame PDB files in ChimeraX (note this is not Chimera 1.13)
https://cxtoolshed.rbvi.ucsf.edu/apps/moleculardynamicsviewer
The main advantage is that it allows use of the VR headset to watch dynamics (via VR on and VR off at command line) For VR, you need to have steamOS with steamVR activated too. With or without VR, it also takes advantage of the new advanced shading available in ChimeraX.
Dr Greg A. Babbitt Life Sciences Rochester Institute of Technology
participants (4)
-
Elaine Meng -
Eric Pettersen -
Gregory Babbitt -
MARIA CLARA BLANES MIRA