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