[chimerax-users] Problems with making movie in chimerax

[Nandish Kumar Khanra]

Hi Vadim,

I see undesired movements in the backbone.

Thanks,
Nandish
________________________________
From: Vadim Kotov <vadim.r.kotov at gmail.com>
Sent: Thursday, May 7, 2020 3:53 AM
To: Nandish Kumar Khanra <nkk2001 at med.cornell.edu>; chimerax-users at cgl.ucsf.edu <chimerax-users at 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




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