Hi Vadim, I see undesired movements in the backbone. Thanks, Nandish ________________________________ From: Vadim Kotov <vadim.r.kotov@gmail.com> Sent: Thursday, May 7, 2020 3:53 AM To: Nandish Kumar Khanra <nkk2001@med.cornell.edu>; chimerax-users@cgl.ucsf.edu <chimerax-users@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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMDaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=DpAiumlSV5DBIb-ActN_MUx1-7a6RRLN7Qol_bll2YM&m=IsmQ77W97aJqs0Toj673P4QrJh2nVWBFCV52TDfxEt8&s=6WWD_8Xmy9JnIo4t-kRnT0pcL83E1BuvevczmsPSuYg&e=>