Friends, I am using MD movie with chimera to see the motion of a single pdb containing 25 models. I kept the play back speed at low value, then recorded the movie. But the movie comes very fast. I guess there is no related functionality between playback speed and the speed with which the movie is recorded. 1) How can i record a movie with low playback speed. 2) Is it possible to split the chimera screen in to two halfes or as quadrants (like in sybyl) and then load the molecules wherever we want. Now why i need it ?. I have two pdb files (each consisiting of 25 models). If i can split the chimera screen, i would like to load pdb1 left and pdb2 in rigth side using MD movie, then record the movie. Any better idea than this to achieve the same would be highly appreciated. 3) Kindly suggest me some better setting to record a movie with high clarity based on your experience. Thanks, Bala
Hi Bala, Now to your question #2. The short answer is no. However, there are some possible approaches, requiring various levels of effort: (A) If it is OK if the two playbacks are not exactly synchronized (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can just open the two files by starting MD Movie twice. Then you will have two playback controllers. For testing, I used NMR ensemble PDB entries 1g1p and 1g1z. These have 18 structures each. While just showing one frame of each (not playing through the frames), I used "mm #0 #1" to fit them into the same orientation. Then I resized the Chimera window to make it longer horizontally and moved one model to the left and the other to the right. Something like these commands (using version 1.4, a daily build): move x -13 models #0 move x 13 models #1 Of course, you would also set colors, display styles, etc. as you want for the movie. Because these two structures are the same size, they play back at about the same speed if I put the two "Playback speed" sliders in the same place. I put both at the far left. If your two structures don't play back at nearly the same speed, move the sliders to try to make them update at the same rate. Now play back continuously for one ensemble. For the other one, stop the playback, choose File... Record movie and proceed as you have been doing. The movie will step through that ensemble, and the other one will just happen to be changing at the same time. Tada! I will send you the Quicktime movie from my test in a separate message. (B) If you need frame 1 with 1, 2 with 2, etc. it is much more effort. I can think of two different routes. (1) just open one ensemble and record with MD Movie, using recording options to control the name and location of the saved image files and the encoding option to keep those files rather than deleting them after encoding a movie. Do the same for the other ensemble. Then with some separate image-processing program combine the first image from each into a new first image with both side by side, etc. for the whole set of saved images. Then encode the new set of combined images into a movie. This would need to be done outside of Chimera, but I believe you could use the software embedded in Chimera to do it. I think the Reply Log shows what command is being used to encode the movie and you could use an analogous command in your system shell or terminal to do it. I haven't done this myself, however. (2) instead create a combined PDB file where each MODEL has both structures side by side. First you'd have to open the two files in Chimera, do any fitting and moving as described in (A), then save PDB for one ensemble "relative to" the other model. Then there would be a lot of painful editing to combine the coordinates into one multi-MODEL file. It would probably require renumbering so that there are not duplicate residues within a single MODEL. Then open that new file with MD Movie as a single trajectory, proceed with recording a movie. As for #3, I am not expert in this area. My general impression is that you could start with the default settings. If that does not look as nice as you want, you could try increasing the bitrate in the encoding options. It is always a trade-off of size and quality, however (nicer looking -> bigger file). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote:
Friends, I am using MD movie with chimera to see the motion of a single pdb containing 25 models. I kept the play back speed at low value, then recorded the movie. But the movie comes very fast. I guess there is no related functionality between playback speed and the speed with which the movie is recorded.
1) How can i record a movie with low playback speed.
2) Is it possible to split the chimera screen in to two halfes or as quadrants (like in sybyl) and then load the molecules wherever we want. Now why i need it ?. I have two pdb files (each consisiting of 25 models). If i can split the chimera screen, i would like to load pdb1 left and pdb2 in rigth side using MD movie, then record the movie. Any better idea than this to achieve the same would be highly appreciated.
3) Kindly suggest me some better setting to record a movie with high clarity based on your experience.
Thanks, Bala
I think another approach is just to forget about MD Movie. Open the two ensembles using regular File..Open or the "open" command. Position one ensemble on the left side and one on the right. Then use a script like this: movie record ... ~disp; disp #0,25; wait 5 ~disp; disp #1,26; wait 5 ... ~disp; disp #24,49; wait 5 movie stop ... movie encode ... to record your movie. --Eric On Apr 16, 2009, at 10:47 AM, Elaine Meng wrote:
Hi Bala, Now to your question #2. The short answer is no. However, there are some possible approaches, requiring various levels of effort:
(A) If it is OK if the two playbacks are not exactly synchronized (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can just open the two files by starting MD Movie twice. Then you will have two playback controllers. For testing, I used NMR ensemble PDB entries 1g1p and 1g1z. These have 18 structures each. While just showing one frame of each (not playing through the frames), I used "mm #0 #1" to fit them into the same orientation. Then I resized the Chimera window to make it longer horizontally and moved one model to the left and the other to the right. Something like these commands (using version 1.4, a daily build): move x -13 models #0 move x 13 models #1 Of course, you would also set colors, display styles, etc. as you want for the movie. Because these two structures are the same size, they play back at about the same speed if I put the two "Playback speed" sliders in the same place. I put both at the far left. If your two structures don't play back at nearly the same speed, move the sliders to try to make them update at the same rate. Now play back continuously for one ensemble. For the other one, stop the playback, choose File... Record movie and proceed as you have been doing. The movie will step through that ensemble, and the other one will just happen to be changing at the same time. Tada! I will send you the Quicktime movie from my test in a separate message.
(B) If you need frame 1 with 1, 2 with 2, etc. it is much more effort. I can think of two different routes. (1) just open one ensemble and record with MD Movie, using recording options to control the name and location of the saved image files and the encoding option to keep those files rather than deleting them after encoding a movie. Do the same for the other ensemble. Then with some separate image-processing program combine the first image from each into a new first image with both side by side, etc. for the whole set of saved images. Then encode the new set of combined images into a movie. This would need to be done outside of Chimera, but I believe you could use the software embedded in Chimera to do it. I think the Reply Log shows what command is being used to encode the movie and you could use an analogous command in your system shell or terminal to do it. I haven't done this myself, however. (2) instead create a combined PDB file where each MODEL has both structures side by side. First you'd have to open the two files in Chimera, do any fitting and moving as described in (A), then save PDB for one ensemble "relative to" the other model. Then there would be a lot of painful editing to combine the coordinates into one multi-MODEL file. It would probably require renumbering so that there are not duplicate residues within a single MODEL. Then open that new file with MD Movie as a single trajectory, proceed with recording a movie.
As for #3, I am not expert in this area. My general impression is that you could start with the default settings. If that does not look as nice as you want, you could try increasing the bitrate in the encoding options. It is always a trade-off of size and quality, however (nicer looking -> bigger file).
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote:
Friends, I am using MD movie with chimera to see the motion of a single pdb containing 25 models. I kept the play back speed at low value, then recorded the movie. But the movie comes very fast. I guess there is no related functionality between playback speed and the speed with which the movie is recorded.
1) How can i record a movie with low playback speed.
2) Is it possible to split the chimera screen in to two halfes or as quadrants (like in sybyl) and then load the molecules wherever we want. Now why i need it ?. I have two pdb files (each consisiting of 25 models). If i can split the chimera screen, i would like to load pdb1 left and pdb2 in rigth side using MD movie, then record the movie. Any better idea than this to achieve the same would be highly appreciated.
3) Kindly suggest me some better setting to record a movie with high clarity based on your experience.
Thanks, Bala
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Bala, As Elaine said increasing the bitrate is the most direct way to better movie quality. The value is in Kbits/sec and default is 2000, and 6000 is better but produces a movie file 3 times bigger. Also the supersample option can be set to 3x3 to produce smoother lines and edges with no increase in file size. http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html Tom Elaine Meng wrote:
Hi Bala, Now to your question #2. The short answer is no. However, there are some possible approaches, requiring various levels of effort:
(A) If it is OK if the two playbacks are not exactly synchronized (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can just open the two files by starting MD Movie twice. Then you will have two playback controllers. For testing, I used NMR ensemble PDB entries 1g1p and 1g1z. These have 18 structures each. While just showing one frame of each (not playing through the frames), I used "mm #0 #1" to fit them into the same orientation. Then I resized the Chimera window to make it longer horizontally and moved one model to the left and the other to the right. Something like these commands (using version 1.4, a daily build): move x -13 models #0 move x 13 models #1 Of course, you would also set colors, display styles, etc. as you want for the movie. Because these two structures are the same size, they play back at about the same speed if I put the two "Playback speed" sliders in the same place. I put both at the far left. If your two structures don't play back at nearly the same speed, move the sliders to try to make them update at the same rate. Now play back continuously for one ensemble. For the other one, stop the playback, choose File... Record movie and proceed as you have been doing. The movie will step through that ensemble, and the other one will just happen to be changing at the same time. Tada! I will send you the Quicktime movie from my test in a separate message.
(B) If you need frame 1 with 1, 2 with 2, etc. it is much more effort. I can think of two different routes. (1) just open one ensemble and record with MD Movie, using recording options to control the name and location of the saved image files and the encoding option to keep those files rather than deleting them after encoding a movie. Do the same for the other ensemble. Then with some separate image-processing program combine the first image from each into a new first image with both side by side, etc. for the whole set of saved images. Then encode the new set of combined images into a movie. This would need to be done outside of Chimera, but I believe you could use the software embedded in Chimera to do it. I think the Reply Log shows what command is being used to encode the movie and you could use an analogous command in your system shell or terminal to do it. I haven't done this myself, however. (2) instead create a combined PDB file where each MODEL has both structures side by side. First you'd have to open the two files in Chimera, do any fitting and moving as described in (A), then save PDB for one ensemble "relative to" the other model. Then there would be a lot of painful editing to combine the coordinates into one multi-MODEL file. It would probably require renumbering so that there are not duplicate residues within a single MODEL. Then open that new file with MD Movie as a single trajectory, proceed with recording a movie.
As for #3, I am not expert in this area. My general impression is that you could start with the default settings. If that does not look as nice as you want, you could try increasing the bitrate in the encoding options. It is always a trade-off of size and quality, however (nicer looking -> bigger file).
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote:
Friends, I am using MD movie with chimera to see the motion of a single pdb containing 25 models. I kept the play back speed at low value, then recorded the movie. But the movie comes very fast. I guess there is no related functionality between playback speed and the speed with which the movie is recorded.
1) How can i record a movie with low playback speed.
2) Is it possible to split the chimera screen in to two halfes or as quadrants (like in sybyl) and then load the molecules wherever we want. Now why i need it ?. I have two pdb files (each consisiting of 25 models). If i can split the chimera screen, i would like to load pdb1 left and pdb2 in rigth side using MD movie, then record the movie. Any better idea than this to achieve the same would be highly appreciated.
3) Kindly suggest me some better setting to record a movie with high clarity based on your experience.
Thanks, Bala
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Eric's approach is MUCH better than what I suggested, especially for these relatively small ensembles and if you want them to be synchronized. I would probably modify his approach slightly by setting up all the display, styles, and colors beforehand and then just using modeldisplay to toggle which models are shown and hidden. Also, in Bala's case, each ensemble is one PDB file, so the individual structures would be submodels. The show/hide commands would look something like this: ~modeldisp; modeldisp #0.1,1.1; wait 5 ~modeldisp; modeldisp #0.2,1.2; wait 5 On Apr 16, 2009, at 10:58 AM, Eric Pettersen wrote:
I think another approach is just to forget about MD Movie. Open the two ensembles using regular File..Open or the "open" command. Position one ensemble on the left side and one on the right. Then use a script like this:
movie record ... ~disp; disp #0,25; wait 5 ~disp; disp #1,26; wait 5 ... ~disp; disp #24,49; wait 5 movie stop ... movie encode ...
to record your movie.
--Eric
On Apr 16, 2009, at 10:47 AM, Elaine Meng wrote:
Hi Bala, Now to your question #2. The short answer is no. However, there are some possible approaches, requiring various levels of effort:
(A) If it is OK if the two playbacks are not exactly synchronized (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can just open the two files by starting MD Movie twice. Then you will have two playback controllers. For testing, I used NMR ensemble PDB entries 1g1p and 1g1z. These have 18 structures each. While just showing one frame of each (not playing through the frames), I used "mm #0 #1" to fit them into the same orientation. Then I resized the Chimera window to make it longer horizontally and moved one model to the left and the other to the right. Something like these commands (using version 1.4, a daily build): move x -13 models #0 move x 13 models #1 Of course, you would also set colors, display styles, etc. as you want for the movie. Because these two structures are the same size, they play back at about the same speed if I put the two "Playback speed" sliders in the same place. I put both at the far left. If your two structures don't play back at nearly the same speed, move the sliders to try to make them update at the same rate. Now play back continuously for one ensemble. For the other one, stop the playback, choose File... Record movie and proceed as you have been doing. The movie will step through that ensemble, and the other one will just happen to be changing at the same time. Tada! I will send you the Quicktime movie from my test in a separate message.
(B) If you need frame 1 with 1, 2 with 2, etc. it is much more effort. I can think of two different routes. (1) just open one ensemble and record with MD Movie, using recording options to control the name and location of the saved image files and the encoding option to keep those files rather than deleting them after encoding a movie. Do the same for the other ensemble. Then with some separate image-processing program combine the first image from each into a new first image with both side by side, etc. for the whole set of saved images. Then encode the new set of combined images into a movie. This would need to be done outside of Chimera, but I believe you could use the software embedded in Chimera to do it. I think the Reply Log shows what command is being used to encode the movie and you could use an analogous command in your system shell or terminal to do it. I haven't done this myself, however. (2) instead create a combined PDB file where each MODEL has both structures side by side. First you'd have to open the two files in Chimera, do any fitting and moving as described in (A), then save PDB for one ensemble "relative to" the other model. Then there would be a lot of painful editing to combine the coordinates into one multi- MODEL file. It would probably require renumbering so that there are not duplicate residues within a single MODEL. Then open that new file with MD Movie as a single trajectory, proceed with recording a movie.
As for #3, I am not expert in this area. My general impression is that you could start with the default settings. If that does not look as nice as you want, you could try increasing the bitrate in the encoding options. It is always a trade-off of size and quality, however (nicer looking -> bigger file).
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote:
Friends, I am using MD movie with chimera to see the motion of a single pdb containing 25 models. I kept the play back speed at low value, then recorded the movie. But the movie comes very fast. I guess there is no related functionality between playback speed and the speed with which the movie is recorded.
1) How can i record a movie with low playback speed.
2) Is it possible to split the chimera screen in to two halfes or as quadrants (like in sybyl) and then load the molecules wherever we want. Now why i need it ?. I have two pdb files (each consisiting of 25 models). If i can split the chimera screen, i would like to load pdb1 left and pdb2 in rigth side using MD movie, then record the movie. Any better idea than this to achieve the same would be highly appreciated.
3) Kindly suggest me some better setting to record a movie with high clarity based on your experience.
Thanks, Bala
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine, This movie recording would be simpler if there was a Chimera command to play an MD trajectory. I've long needed that for animation scripts. I've added that to the list of feature requests: http://socrates2.cgl.ucsf.edu/trac/chimera/wiki/requests Tom Elaine Meng wrote:
Eric's approach is MUCH better than what I suggested, especially for these relatively small ensembles and if you want them to be synchronized. I would probably modify his approach slightly by setting up all the display, styles, and colors beforehand and then just using modeldisplay to toggle which models are shown and hidden. Also, in Bala's case, each ensemble is one PDB file, so the individual structures would be submodels. The show/hide commands would look something like this:
~modeldisp; modeldisp #0.1,1.1; wait 5 ~modeldisp; modeldisp #0.2,1.2; wait 5
On Apr 16, 2009, at 10:58 AM, Eric Pettersen wrote:
I think another approach is just to forget about MD Movie. Open the two ensembles using regular File..Open or the "open" command. Position one ensemble on the left side and one on the right. Then use a script like this:
movie record ... ~disp; disp #0,25; wait 5 ~disp; disp #1,26; wait 5 ... ~disp; disp #24,49; wait 5 movie stop ... movie encode ...
to record your movie.
--Eric
On Apr 16, 2009, at 10:47 AM, Elaine Meng wrote:
Hi Bala, Now to your question #2. The short answer is no. However, there are some possible approaches, requiring various levels of effort:
(A) If it is OK if the two playbacks are not exactly synchronized (don't need frame 1 and frame 1 together, 2 and 2, etc.), you can just open the two files by starting MD Movie twice. Then you will have two playback controllers. For testing, I used NMR ensemble PDB entries 1g1p and 1g1z. These have 18 structures each. While just showing one frame of each (not playing through the frames), I used "mm #0 #1" to fit them into the same orientation. Then I resized the Chimera window to make it longer horizontally and moved one model to the left and the other to the right. Something like these commands (using version 1.4, a daily build): move x -13 models #0 move x 13 models #1 Of course, you would also set colors, display styles, etc. as you want for the movie. Because these two structures are the same size, they play back at about the same speed if I put the two "Playback speed" sliders in the same place. I put both at the far left. If your two structures don't play back at nearly the same speed, move the sliders to try to make them update at the same rate. Now play back continuously for one ensemble. For the other one, stop the playback, choose File... Record movie and proceed as you have been doing. The movie will step through that ensemble, and the other one will just happen to be changing at the same time. Tada! I will send you the Quicktime movie from my test in a separate message.
(B) If you need frame 1 with 1, 2 with 2, etc. it is much more effort. I can think of two different routes. (1) just open one ensemble and record with MD Movie, using recording options to control the name and location of the saved image files and the encoding option to keep those files rather than deleting them after encoding a movie. Do the same for the other ensemble. Then with some separate image-processing program combine the first image from each into a new first image with both side by side, etc. for the whole set of saved images. Then encode the new set of combined images into a movie. This would need to be done outside of Chimera, but I believe you could use the software embedded in Chimera to do it. I think the Reply Log shows what command is being used to encode the movie and you could use an analogous command in your system shell or terminal to do it. I haven't done this myself, however. (2) instead create a combined PDB file where each MODEL has both structures side by side. First you'd have to open the two files in Chimera, do any fitting and moving as described in (A), then save PDB for one ensemble "relative to" the other model. Then there would be a lot of painful editing to combine the coordinates into one multi- MODEL file. It would probably require renumbering so that there are not duplicate residues within a single MODEL. Then open that new file with MD Movie as a single trajectory, proceed with recording a movie.
As for #3, I am not expert in this area. My general impression is that you could start with the default settings. If that does not look as nice as you want, you could try increasing the bitrate in the encoding options. It is always a trade-off of size and quality, however (nicer looking -> bigger file).
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html
On Apr 16, 2009, at 3:32 AM, Bala subramanian wrote:
Friends, I am using MD movie with chimera to see the motion of a single pdb containing 25 models. I kept the play back speed at low value, then recorded the movie. But the movie comes very fast. I guess there is no related functionality between playback speed and the speed with which the movie is recorded.
1) How can i record a movie with low playback speed.
2) Is it possible to split the chimera screen in to two halfes or as quadrants (like in sybyl) and then load the molecules wherever we want. Now why i need it ?. I have two pdb files (each consisiting of 25 models). If i can split the chimera screen, i would like to load pdb1 left and pdb2 in rigth side using MD movie, then record the movie. Any better idea than this to achieve the same would be highly appreciated.
3) Kindly suggest me some better setting to record a movie with high clarity based on your experience.
Thanks, Bala
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Bala subramanian -
Elaine Meng -
Eric Pettersen -
Thomas Goddard