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Hi Vadim,</div>
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I see undesired movements in the backbone.</div>
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Thanks,</div>
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Nandish</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Vadim Kotov <vadim.r.kotov@gmail.com><br>
<b>Sent:</b> Thursday, May 7, 2020 3:53 AM<br>
<b>To:</b> Nandish Kumar Khanra <nkk2001@med.cornell.edu>; chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [EXTERNAL] Re: [chimerax-users] Problems with making movie in chimerax</font>
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<div class="x_moz-cite-prefix">Dear <span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">
Nandish,</span></div>
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<div class="x_moz-cite-prefix"><span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial"> 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.</span></div>
<div class="x_moz-cite-prefix"><span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial"><br>
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<div class="x_moz-cite-prefix"><span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">Best wishes,<br>
Vadim Kotov</span></div>
<div class="x_moz-cite-prefix"><span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">Postdoctoral fellow<br>
EMBL Hamburg<br>
</span></div>
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<div class="x_moz-cite-prefix">On 07/05/2020 00:33, Nandish Kumar Khanra wrote:<br>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">Hello all,</span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">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. </span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">Aligned two models using matchmaker,</span></li></ul>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">mm #1 to #2 pair ss ss false</span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">make morph</span></li></ul>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">morph #1,2 frames 100 play false cartesian true</span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">make movie</span></li></ul>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">movie record size 1000,1000</span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">coordset #3</span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">wait 100</span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">movie encode output ~/Desktop/movie1.mp4 quality higher framerate 25 roundTrip true</span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">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?</span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">Thanks,</span></p>
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<span style="margin-top:0pt; margin-bottom:0pt; background-position:initial initial; background-repeat:initial initial">Nandish</span></p>
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