Problems with making movie in chimerax
Hello all, I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie. * Aligned two models using matchmaker, mm #1 to #2 pair ss ss false * make morph morph #1,2 frames 100 play false cartesian true * make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this? Thanks, Nandish
Hi Nandish, This boils down to a morph question. Omitting the complication of the movie, just look at the trajectory and the two input structures. Unless you moved the morph trajectory model separately after it was created, the position at the first frame of the morph trajectory should be exactly the same as the position in the starting structure input to the morph calculation, and the position at the last frame of the morph trajectory should be exactly the same as the position in the ending structure input to the morph calculation. I think the problem is that the morph trajectory will include 101 frames. This is explained in the help page, that when you specify "frames N" the total number of frames in the trajectory = 1 + N(number of stages). Your morph trajectory has one stage, one conformational change. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> I didn't review the help page but just tried an example with your same commands, and when the morph calculated there is a message shown in the log that it has 101 frames, and the playback slider title bar also says it has 101 frames. So your wait 100 command only ensures the first 100 frames are in the movie, not all 101. 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 6, 2020, at 3:33 PM, Nandish Kumar Khanra <nkk2001@med.cornell.edu> wrote:
Hello all,
I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie.
• Aligned two models using matchmaker, mm #1 to #2 pair ss ss false
• make morph morph #1,2 frames 100 play false cartesian true
• make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true
The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this?
Thanks, Nandish
Hi Elaine, Thanks for your reply and for pointing out the total number of frames in the trajectory. The first and the end frames are the same as the start and end structures. however, I see the movement of few helices in the intermediate frames but these helices should not move in the intermediate frames also. Do you know how to overcome this? Thanks, Nandish ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, May 6, 2020 6:55 PM To: Nandish Kumar Khanra <nkk2001@med.cornell.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax Hi Nandish, This boils down to a morph question. Omitting the complication of the movie, just look at the trajectory and the two input structures. Unless you moved the morph trajectory model separately after it was created, the position at the first frame of the morph trajectory should be exactly the same as the position in the starting structure input to the morph calculation, and the position at the last frame of the morph trajectory should be exactly the same as the position in the ending structure input to the morph calculation. I think the problem is that the morph trajectory will include 101 frames. This is explained in the help page, that when you specify "frames N" the total number of frames in the trajectory = 1 + N(number of stages). Your morph trajectory has one stage, one conformational change. <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > I didn't review the help page but just tried an example with your same commands, and when the morph calculated there is a message shown in the log that it has 101 frames, and the playback slider title bar also says it has 101 frames. So your wait 100 command only ensures the first 100 frames are in the movie, not all 101. 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 6, 2020, at 3:33 PM, Nandish Kumar Khanra <nkk2001@med.cornell.edu> wrote:
Hello all,
I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie.
• Aligned two models using matchmaker, mm #1 to #2 pair ss ss false
• make morph morph #1,2 frames 100 play false cartesian true
• make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true
The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this?
Thanks, Nandish
Hi Nandish, Not specifically, but you can try changing morph parameter options and values to see how they affect the intermediate conformations. I'd probably try changing the coreFraction and/or using "cartesian true" first, but it's not easy to predict what will help. Trial and error! <http://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html#morph-parameters> Elaine
On May 6, 2020, at 4:27 PM, Nandish Kumar Khanra <nkk2001@med.cornell.edu> wrote:
Hi Elaine,
Thanks for your reply and for pointing out the total number of frames in the trajectory. The first and the end frames are the same as the start and end structures. however, I see the movement of few helices in the intermediate frames but these helices should not move in the intermediate frames also. Do you know how to overcome this?
Thanks, Nandish From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, May 6, 2020 6:55 PM To: Nandish Kumar Khanra <nkk2001@med.cornell.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax
Hi Nandish, This boils down to a morph question. Omitting the complication of the movie, just look at the trajectory and the two input structures. Unless you moved the morph trajectory model separately after it was created, the position at the first frame of the morph trajectory should be exactly the same as the position in the starting structure input to the morph calculation, and the position at the last frame of the morph trajectory should be exactly the same as the position in the ending structure input to the morph calculation.
I think the problem is that the morph trajectory will include 101 frames. This is explained in the help page, that when you specify "frames N" the total number of frames in the trajectory = 1 + N(number of stages). Your morph trajectory has one stage, one conformational change. <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... >
I didn't review the help page but just tried an example with your same commands, and when the morph calculated there is a message shown in the log that it has 101 frames, and the playback slider title bar also says it has 101 frames.
So your wait 100 command only ensures the first 100 frames are in the movie, not all 101.
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 6, 2020, at 3:33 PM, Nandish Kumar Khanra <nkk2001@med.cornell.edu> wrote:
Hello all,
I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie.
• Aligned two models using matchmaker, mm #1 to #2 pair ss ss false
• make morph morph #1,2 frames 100 play false cartesian true
• make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true
The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this?
Thanks, Nandish
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Elaine, Thanks for your reply. I will try these. Best, Nandish ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, May 6, 2020 7:36 PM To: Nandish Kumar Khanra <nkk2001@med.cornell.edu> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax Hi Nandish, Not specifically, but you can try changing morph parameter options and values to see how they affect the intermediate conformations. I'd probably try changing the coreFraction and/or using "cartesian true" first, but it's not easy to predict what will help. Trial and error! <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... > Elaine
On May 6, 2020, at 4:27 PM, Nandish Kumar Khanra <nkk2001@med.cornell.edu> wrote:
Hi Elaine,
Thanks for your reply and for pointing out the total number of frames in the trajectory. The first and the end frames are the same as the start and end structures. however, I see the movement of few helices in the intermediate frames but these helices should not move in the intermediate frames also. Do you know how to overcome this?
Thanks, Nandish From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, May 6, 2020 6:55 PM To: Nandish Kumar Khanra <nkk2001@med.cornell.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax
Hi Nandish, This boils down to a morph question. Omitting the complication of the movie, just look at the trajectory and the two input structures. Unless you moved the morph trajectory model separately after it was created, the position at the first frame of the morph trajectory should be exactly the same as the position in the starting structure input to the morph calculation, and the position at the last frame of the morph trajectory should be exactly the same as the position in the ending structure input to the morph calculation.
I think the problem is that the morph trajectory will include 101 frames. This is explained in the help page, that when you specify "frames N" the total number of frames in the trajectory = 1 + N(number of stages). Your morph trajectory has one stage, one conformational change. <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... >
I didn't review the help page but just tried an example with your same commands, and when the morph calculated there is a message shown in the log that it has 101 frames, and the playback slider title bar also says it has 101 frames.
So your wait 100 command only ensures the first 100 frames are in the movie, not all 101.
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 6, 2020, at 3:33 PM, Nandish Kumar Khanra <nkk2001@med.cornell.edu> wrote:
Hello all,
I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie.
• Aligned two models using matchmaker, mm #1 to #2 pair ss ss false
• make morph morph #1,2 frames 100 play false cartesian true
• make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true
The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this?
Thanks, Nandish
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailm...
In general, if the start and end conformations are exactly the same for part of a structure then it should not move at all in a morph. If they are slightly different then it should move only slightly. If you are getting a large motion between start and end conformations that are only slightly different then that sounds like a bug. You could provide start and end structures or a movie clip to show what you are talking about. Tom
On May 6, 2020, at 4:40 PM, Nandish Kumar Khanra <nkk2001@med.cornell.edu <mailto:nkk2001@med.cornell.edu>> wrote:
Hi Elaine,
Thanks for your reply. I will try these.
Best, Nandish From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Wednesday, May 6, 2020 7:36 PM To: Nandish Kumar Khanra <nkk2001@med.cornell.edu <mailto:nkk2001@med.cornell.edu>> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: [EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax
Hi Nandish, Not specifically, but you can try changing morph parameter options and values to see how they affect the intermediate conformations. I'd probably try changing the coreFraction and/or using "cartesian true" first, but it's not easy to predict what will help. Trial and error!
< <applewebdata://983DE590-2E0C-4A27-AB71-72968B838203>https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d...> >
Elaine
On May 6, 2020, at 4:27 PM, Nandish Kumar Khanra <nkk2001@med.cornell.edu <mailto:nkk2001@med.cornell.edu>> wrote:
Hi Elaine,
Thanks for your reply and for pointing out the total number of frames in the trajectory. The first and the end frames are the same as the start and end structures. however, I see the movement of few helices in the intermediate frames but these helices should not move in the intermediate frames also. Do you know how to overcome this?
Thanks, Nandish From: Elaine Meng <meng@cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> Sent: Wednesday, May 6, 2020 6:55 PM To: Nandish Kumar Khanra <nkk2001@med.cornell.edu <mailto:nkk2001@med.cornell.edu>> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> Subject: [EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax
Hi Nandish, This boils down to a morph question. Omitting the complication of the movie, just look at the trajectory and the two input structures. Unless you moved the morph trajectory model separately after it was created, the position at the first frame of the morph trajectory should be exactly the same as the position in the starting structure input to the morph calculation, and the position at the last frame of the morph trajectory should be exactly the same as the position in the ending structure input to the morph calculation.
I think the problem is that the morph trajectory will include 101 frames. This is explained in the help page, that when you specify "frames N" the total number of frames in the trajectory = 1 + N(number of stages). Your morph trajectory has one stage, one conformational change. < <applewebdata://983DE590-2E0C-4A27-AB71-72968B838203>https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d... <https://urldefense.proofpoint.com/v2/url?u=http-3A__rbvi.ucsf.edu_chimerax_d...> >
I didn't review the help page but just tried an example with your same commands, and when the morph calculated there is a message shown in the log that it has 101 frames, and the playback slider title bar also says it has 101 frames.
So your wait 100 command only ensures the first 100 frames are in the movie, not all 101.
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 6, 2020, at 3:33 PM, Nandish Kumar Khanra <nkk2001@med.cornell.edu <mailto:nkk2001@med.cornell.edu>> wrote:
Hello all,
I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie.
• Aligned two models using matchmaker, mm #1 to #2 pair ss ss false
• make morph morph #1,2 frames 100 play false cartesian true
• make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true
The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this?
Thanks, Nandish
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailm... <https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailm...>
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
Dear Nandish, do you see undesired movements in the side-chains or in the backbone? If it is only side-chains, than it could happen that the atoms are numbered differently in the two conformations. For instance, if a Phe residue is numbered clock-wise in conformation A, and counterclockwise in conformation B, then during a morph the side-chain will perform a 360 degree rotation. In this case you would need to manually edit atom names in one of the PDB files. Best wishes, Vadim Kotov Postdoctoral fellow EMBL Hamburg On 07/05/2020 00:33, Nandish Kumar Khanra wrote:
Hello all,
I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie.
* Aligned two models using matchmaker,
mm #1 to #2 pair ss ss false
* make morph
morph #1,2 frames 100 play false cartesian true
* make movie
movie record size 1000,1000
coordset #3
wait 100
movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true
The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this?
Thanks,
Nandish
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Vadim, I see undesired movements in the backbone. Thanks, Nandish ________________________________ From: Vadim Kotov <vadim.r.kotov@gmail.com> Sent: Thursday, May 7, 2020 3:53 AM To: Nandish Kumar Khanra <nkk2001@med.cornell.edu>; chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax Dear Nandish, do you see undesired movements in the side-chains or in the backbone? If it is only side-chains, than it could happen that the atoms are numbered differently in the two conformations. For instance, if a Phe residue is numbered clock-wise in conformation A, and counterclockwise in conformation B, then during a morph the side-chain will perform a 360 degree rotation. In this case you would need to manually edit atom names in one of the PDB files. Best wishes, Vadim Kotov Postdoctoral fellow EMBL Hamburg On 07/05/2020 00:33, Nandish Kumar Khanra wrote: Hello all, I want to make a movie of a multi-domain protein between two functional states using Chimerax. One domain undergoes drastic conformational change while there is virtually no structural change in another domain. I did the following steps to make the movie. * Aligned two models using matchmaker, mm #1 to #2 pair ss ss false * make morph morph #1,2 frames 100 play false cartesian true * make movie movie record size 1000,1000 coordset #3 wait 100 movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true The stationary domain of two functional states aligned perfectly after structural alignment, but I do see motions in that domain in the movie. Am I doing anything wrong? Is there a way to overcome this? Thanks, Nandish _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMDaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=DpAiumlSV5DBIb-ActN_MUx1-7a6RRLN7Qol_bll2YM&m=IsmQ77W97aJqs0Toj673P4QrJh2nVWBFCV52TDfxEt8&s=6WWD_8Xmy9JnIo4t-kRnT0pcL83E1BuvevczmsPSuYg&e=>
participants (4)
-
Elaine Meng -
Nandish Kumar Khanra -
Tom Goddard -
Vadim Kotov