Chimera morph colors with morph conformations
Hello, I'm trying to create a movie with morph conformations. I wonder if it's possible to morph the colors, or change colors midway through, going from one conformation into the other. Please feel free to contribute any ideas or thoughts on how to make my movie clearer and more visually aesthetic. Thanks.
Hello Ahmad, To answer your previous question, you can play back the morph trajectory (or other trajectories) with the “coordset” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> My approach to making movies with morphs in them is to use command scripts. Here are two examples of such movies that you can play, and links to their Chimera command scripts: (1) Morphing between the inactive and activated conformations of the FGFR1 kinase domain. <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#kinase-morph> (2) Ball-and-socket motion. <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#trmovie> However, I haven’t made a movie where I morph the color at the same time as playing the morph trajectory. According to my testing just now, it cannot be done in commands. Instead you have to use the Animations dialog. You would have to show one step (the starting point) of the trajectory with one color, save a scene, then show the endpoint step, change color, and then save a second scene. Then you have to move both scenes down to the timeline and play (and record if you want). There could be other scenes on the timeline that are not different steps in morphing, with other changes in display, coloring, labels, etc. You can use “scene” command to save and restore scenes in a command script, but I could not find any way that would gradually change the color at the same time as playing the morph with “coordset.” I personally prefer to use command scripts rather than saving a giant session with all the scenes in the timeline. However, the timeline and graphical Animation tool may be easier to use if you are not experienced with commands. You would still have to spend some time learning how to use the Animation tool. Here is its help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/animation/frameanimation.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 Sep 26, 2018, at 7:34 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Hello,
I'm trying to create a movie with morph conformations. I wonder if it's possible to morph the colors, or change colors midway through, going from one conformation into the other.
Please feel free to contribute any ideas or thoughts on how to make my movie clearer and more visually aesthetic.
Thanks.
Thank you so much, is there a way to set the frame speed with coordset? On Wed, Sep 26, 2018 at 12:59 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Ahmad, To answer your previous question, you can play back the morph trajectory (or other trajectories) with the “coordset” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
My approach to making movies with morphs in them is to use command scripts. Here are two examples of such movies that you can play, and links to their Chimera command scripts:
(1) Morphing between the inactive and activated conformations of the FGFR1 kinase domain. <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#kinase-morph>
(2) Ball-and-socket motion. <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#trmovie>
However, I haven’t made a movie where I morph the color at the same time as playing the morph trajectory. According to my testing just now, it cannot be done in commands. Instead you have to use the Animations dialog. You would have to show one step (the starting point) of the trajectory with one color, save a scene, then show the endpoint step, change color, and then save a second scene. Then you have to move both scenes down to the timeline and play (and record if you want). There could be other scenes on the timeline that are not different steps in morphing, with other changes in display, coloring, labels, etc.
You can use “scene” command to save and restore scenes in a command script, but I could not find any way that would gradually change the color at the same time as playing the morph with “coordset.”
I personally prefer to use command scripts rather than saving a giant session with all the scenes in the timeline. However, the timeline and graphical Animation tool may be easier to use if you are not experienced with commands. You would still have to spend some time learning how to use the Animation tool. Here is its help page: < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/animation/frameani...
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2018, at 7:34 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Hello,
I'm trying to create a movie with morph conformations. I wonder if it's possible to morph the colors, or change colors midway through, going from one conformation into the other.
Please feel free to contribute any ideas or thoughts on how to make my movie clearer and more visually aesthetic.
Thanks.
Hi Ahmad, Sorry no. However, in general movie framerate is not the same as when you are running Chimera, and movie framerate can be controlled with the framerate option of the “movie encode” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html> In our newer program ChimeraX (where most development effort is now), “coordset” does have a “pauseFrames” option to slow down playback: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> … but it is not implemented in Chimera “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> In Chimera. other than just having a slower movie framerate as mentioned above, to show the morph more slowly you would need to create the morph trajectory with more frames. I hope this helps, Elaine
On Sep 26, 2018, at 10:46 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thank you so much, is there a way to set the frame speed with coordset?
Thanks Elaine. I meant the framerate of the molecular movie not the movie that I'm recording. In the molecular movie window, there's a slider that goes from slow to fast. I want to be able to control the speed from the command line as well. Coordset plays the frames from 1 to 21 at the fastest speed. I tried to experiment with the perframe command but couldn't quite get it right. How can I use perframe to play the movie and introduce a wait of a few milliseconds in between frames thus controlling the speed of the molecular movie? Best regards. On Wed, Sep 26, 2018, 5:19 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, Sorry no. However, in general movie framerate is not the same as when you are running Chimera, and movie framerate can be controlled with the framerate option of the “movie encode” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
In our newer program ChimeraX (where most development effort is now), “coordset” does have a “pauseFrames” option to slow down playback: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> … but it is not implemented in Chimera “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
In Chimera. other than just having a slower movie framerate as mentioned above, to show the morph more slowly you would need to create the morph trajectory with more frames.
I hope this helps, Elaine
On Sep 26, 2018, at 10:46 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thank you so much, is there a way to set the frame speed with coordset?
Hi Ahmad, I already answered this question in the previous reply! Again, if your goal is to make a recorded movie file, use one or both of the following: (1) you control framerate in a recorded movie file with “movie encode” command option “framerate”. There is no Chimera command option tthat acts like the MD Movie dialog’s faster-slower slider, and “perframe” doesn’t do it. (2) go back and create the morph trajectory with more steps in it, e.g. spread the motion across 200 steps instead of 20. If you are NOT making a movie file and you only care about interactive playback, there is “set maxframerate” (this is different than what the MD Movie slider does), but it will have absolutely no effect on the speed of a recorded movie file. set maxFrameRate <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#maxframerate> discussion of frame rate and movie speed <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#speed> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2018, at 9:37 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks Elaine. I meant the framerate of the molecular movie not the movie that I'm recording. In the molecular movie window, there's a slider that goes from slow to fast. I want to be able to control the speed from the command line as well.
Coordset plays the frames from 1 to 21 at the fastest speed. I tried to experiment with the perframe command but couldn't quite get it right. How can I use perframe to play the movie and introduce a wait of a few milliseconds in between frames thus controlling the speed of the molecular movie?
Best regards.
On Wed, Sep 26, 2018, 5:19 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, Sorry no. However, in general movie framerate is not the same as when you are running Chimera, and movie framerate can be controlled with the framerate option of the “movie encode” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
In our newer program ChimeraX (where most development effort is now), “coordset” does have a “pauseFrames” option to slow down playback: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> … but it is not implemented in Chimera “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
In Chimera. other than just having a slower movie framerate as mentioned above, to show the morph more slowly you would need to create the morph trajectory with more frames.
I hope this helps, Elaine
On Sep 26, 2018, at 10:46 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thank you so much, is there a way to set the frame speed with coordset?
Hi Ahmad, My experiments just now suggest even “max framerate” may not have much effect on how fast the morph looks in interactive playback. I think you will need to use approach #2: go back and create the morph again, but with more steps. That will slow down the motion during interactive playback (as well as in a recorded movie, if you make one). Best, Elaine
On Sep 27, 2018, at 10:05 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, I already answered this question in the previous reply!
Again, if your goal is to make a recorded movie file, use one or both of the following:
(1) you control framerate in a recorded movie file with “movie encode” command option “framerate”. There is no Chimera command option tthat acts like the MD Movie dialog’s faster-slower slider, and “perframe” doesn’t do it.
(2) go back and create the morph trajectory with more steps in it, e.g. spread the motion across 200 steps instead of 20.
If you are NOT making a movie file and you only care about interactive playback, there is “set maxframerate” (this is different than what the MD Movie slider does), but it will have absolutely no effect on the speed of a recorded movie file.
set maxFrameRate <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#maxframerate>
discussion of frame rate and movie speed <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#speed>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2018, at 9:37 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks Elaine. I meant the framerate of the molecular movie not the movie that I'm recording. In the molecular movie window, there's a slider that goes from slow to fast. I want to be able to control the speed from the command line as well.
Coordset plays the frames from 1 to 21 at the fastest speed. I tried to experiment with the perframe command but couldn't quite get it right. How can I use perframe to play the movie and introduce a wait of a few milliseconds in between frames thus controlling the speed of the molecular movie?
Best regards.
On Wed, Sep 26, 2018, 5:19 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, Sorry no. However, in general movie framerate is not the same as when you are running Chimera, and movie framerate can be controlled with the framerate option of the “movie encode” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
In our newer program ChimeraX (where most development effort is now), “coordset” does have a “pauseFrames” option to slow down playback: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> … but it is not implemented in Chimera “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
In Chimera. other than just having a slower movie framerate as mentioned above, to show the morph more slowly you would need to create the morph trajectory with more frames.
I hope this helps, Elaine
On Sep 26, 2018, at 10:46 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thank you so much, is there a way to set the frame speed with coordset?
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you so much. I think rerecording the morphs is my best option. I wonder however if there's a way to reset the molecular movie to start after each time I play it using coordset. After it's playing, the model is displayed in chimera as the last frame of the movie. On Thu, Sep 27, 2018 at 1:16 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, My experiments just now suggest even “max framerate” may not have much effect on how fast the morph looks in interactive playback. I think you will need to use approach #2: go back and create the morph again, but with more steps. That will slow down the motion during interactive playback (as well as in a recorded movie, if you make one). Best, Elaine
On Sep 27, 2018, at 10:05 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Ahmad, I already answered this question in the previous reply!
Again, if your goal is to make a recorded movie file, use one or both of the following:
(1) you control framerate in a recorded movie file with “movie encode” command option “framerate”. There is no Chimera command option tthat acts like the MD Movie dialog’s faster-slower slider, and “perframe” doesn’t do it.
(2) go back and create the morph trajectory with more steps in it, e.g. spread the motion across 200 steps instead of 20.
If you are NOT making a movie file and you only care about interactive playback, there is “set maxframerate” (this is different than what the MD Movie slider does), but it will have absolutely no effect on the speed of a recorded movie file.
set maxFrameRate < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#maxframerate
discussion of frame rate and movie speed <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#speed>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 26, 2018, at 9:37 PM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thanks Elaine. I meant the framerate of the molecular movie not the movie that I'm recording. In the molecular movie window, there's a slider that goes from slow to fast. I want to be able to control the speed from the command line as well.
Coordset plays the frames from 1 to 21 at the fastest speed. I tried to experiment with the perframe command but couldn't quite get it right. How can I use perframe to play the movie and introduce a wait of a few milliseconds in between frames thus controlling the speed of the molecular movie?
Best regards.
On Wed, Sep 26, 2018, 5:19 PM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi Ahmad, Sorry no. However, in general movie framerate is not the same as when you are running Chimera, and movie framerate can be controlled with the framerate option of the “movie encode” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/movie.html>
In our newer program ChimeraX (where most development effort is now), “coordset” does have a “pauseFrames” option to slow down playback: <http://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> … but it is not implemented in Chimera “coordset”: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
In Chimera. other than just having a slower movie framerate as mentioned above, to show the morph more slowly you would need to create the morph trajectory with more frames.
I hope this helps, Elaine
On Sep 26, 2018, at 10:46 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thank you so much, is there a way to set the frame speed with coordset?
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Ahmad, You can use “coordset” to just go to any individual step of the trajectory that you want (including the first one), and stop there. Or, you could use it to play the trajectory first forward and then backward. See the manual page for several examples: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html> There were also examples in the morphing movie command scripts mentioned a few messages earlier. Best, Elaine
On Sep 28, 2018, at 8:49 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Thank you so much. I think rerecording the morphs is my best option. I wonder however if there's a way to reset the molecular movie to start after each time I play it using coordset. After it's playing, the model is displayed in chimera as the last frame of the movie.
Correction to my previous answer: it is possible to morph colors at the same time as playing the morph trajectory using a command script. For example, if I have scene named “1” which is frame 21 of the morph trajectory in one color, and another scene named “2” which is frame 41 of the morph trajectory in another color, then the following command plays from 21 to 41 while morphing the color at the same time: scene 1 reset; coordset #2 21,41; scene 2 reset 20; wait 20 As to whether morphing the colors at the same time as playing the trajectory is the best way to show what you want, it depends on artistic or personal preferences, so I’ll leave it up to you to decide! Best, Elaine
On Sep 26, 2018, at 9:59 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Ahmad, To answer your previous question, you can play back the morph trajectory (or other trajectories) with the “coordset” command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>
My approach to making movies with morphs in them is to use command scripts. Here are two examples of such movies that you can play, and links to their Chimera command scripts:
(1) Morphing between the inactive and activated conformations of the FGFR1 kinase domain. <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#kinase-morph>
(2) Ball-and-socket motion. <http://www.rbvi.ucsf.edu/chimera/animations/animations.html#trmovie>
However, I haven’t made a movie where I morph the color at the same time as playing the morph trajectory. According to my testing just now, it cannot be done in commands. Instead you have to use the Animations dialog. You would have to show one step (the starting point) of the trajectory with one color, save a scene, then show the endpoint step, change color, and then save a second scene. Then you have to move both scenes down to the timeline and play (and record if you want). There could be other scenes on the timeline that are not different steps in morphing, with other changes in display, coloring, labels, etc.
You can use “scene” command to save and restore scenes in a command script, but I could not find any way that would gradually change the color at the same time as playing the morph with “coordset.”
I personally prefer to use command scripts rather than saving a giant session with all the scenes in the timeline. However, the timeline and graphical Animation tool may be easier to use if you are not experienced with commands. You would still have to spend some time learning how to use the Animation tool. Here is its help page: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/animation/frameanimation.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 Sep 26, 2018, at 7:34 AM, Ahmad Khalifa <underoath006@gmail.com> wrote:
Hello,
I'm trying to create a movie with morph conformations. I wonder if it's possible to morph the colors, or change colors midway through, going from one conformation into the other.
Please feel free to contribute any ideas or thoughts on how to make my movie clearer and more visually aesthetic.
Thanks.
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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