[Chimera-users] morphed conformation movie?

Elaine Meng meng at cgl.ucsf.edu
Thu May 18 09:20:20 PDT 2017

Hi Lothar,
I’m thinking you mean the “MD Movie” playback controller.  If it’s just behind other windows, you could re-raise it from the “active dialogs” section of the Rapid Access screen shown by clicking the lightning-bolt icon near the lower right corner of the Chimera window.

However, if you have saved the session with the morph trajectory and then restored it, that graphical interface doesn’t come back.

Not to worry, though: regardless of whether you have the MD Movie graphical interface, you can play back or jump to individual frames of a trajectory with the “coordset” command.

The “perframe ksdssp” issue is orthogonal to whether or not you are using the graphical interface. Even if you are using the graphical interface, you may need to run ksdssp per-frame as specified in the MD Movie menu: Per-Frame… Define script.

For “coordset” commands, see for example the first movie in our Animation Gallery, including the command file and session file used to make the movie.  The session contains the already-made morph trajectory as model 3 and the command file plays it back, among other things.

There wasn’t too much secondary structure change so I didn’t put ksdssp in that script.  However, I attach a modified script including “perframe ksdssp” and “~perframe” bracketing each of the parts where there was playback with “coordset.”  It also has the movie-recording commented out, so you can just open the session and then open this script kinase-morph-ksdssp.cmd to see it run the content without making any files.

(There is also another example further down in the Animations page, “Ball-and-socket motion” where the included script doesn’t use a pre-existing session but creates the morph before starting to record.)

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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Script contents are just the following lines in plain text:

windowsize 400 400
reset p1
#movie record supersample 3
rock y .9 68; wait
wait 10
perframe ksdssp
coordset #3 1,31; wait 31
coordset #3 32,41; disp :acp; transparency 0 :acp frames 10; wait 10
2dlab change lab visibility show frames 20; wait
disp #0:653,654 at p,oh,o?p; setattr g display false P; wait
rock y .9 136; wait
2dlab change lab visibility hide; wait
~disp #0:653,654 at p,oh,o?p; wait 5
perframe ksdssp
coordset #3 41,50; transparency 100 :acp frames 10; wait 10
~disp :acp
coordset #3 51,81; wait 31
wait 10
#movie stop
#movie encode quality high format h264 output ~/Desktop/kinase-morph3.mp4

> On May 18, 2017, at 8:53 AM, esserlo at helix.nih.gov wrote:
> Hi,
>   I used Tools->Structure Comparison->Morph Conformations and it worked well.
> However, I somehow lost the menu that opens up after the morph is complete.
> Well, I cannot find it. How can you re-open it to run through the morphed
> conformations again ?
> Also is there a commandline version to access the conformations and to re-run
> kdssp on each interpolated conformation? I read you need the perframe command
> for that. Does anyone have a working example ?
> Thanks,
>   Lothar

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