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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