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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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