[chimerax-users] Problems with making movie in chimerax

[Vadim Kotov]

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
>
>
>
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