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<div class="moz-cite-prefix">Dear <span style="margin-top: 0pt;
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background-repeat: initial initial">Nandish,</span></div>
<div class="moz-cite-prefix"><span style="margin-top: 0pt;
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</span></div>
<div class="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="moz-cite-prefix"><span style="margin-top: 0pt;
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</span></div>
<div class="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="moz-cite-prefix"><span style="margin-top: 0pt;
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background-repeat: initial initial">Postdoctoral fellow<br>
EMBL Hamburg<br>
</span></div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix"><br>
</div>
<div class="moz-cite-prefix">On 07/05/2020 00:33, Nandish Kumar
Khanra wrote:<br>
</div>
<blockquote type="cite"
cite="mid:BYAPR06MB5717F037B1963392DA1EA5E6FAA40@BYAPR06MB5717.namprd06.prod.outlook.com">
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<span style="margin-top: 0pt; margin-bottom: 0pt;
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initial initial">Hello all,</span></p>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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<br>
</p>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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<span style="margin-top: 0pt; margin-bottom: 0pt;
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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>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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<br>
</p>
<ul style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<li style="margin-top: 0pt; margin-bottom: 0pt;
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initial initial">
<span style="margin-top: 0pt; margin-bottom: 0pt;
background-position: initial initial; background-repeat:
initial initial">Aligned two models using matchmaker,</span></li>
</ul>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<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>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<br>
</p>
<ul style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<li style="margin-top: 0pt; margin-bottom: 0pt;
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initial initial">
<span style="margin-top: 0pt; margin-bottom: 0pt;
background-position: initial initial; background-repeat:
initial initial">make morph</span></li>
</ul>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<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>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<br>
</p>
<ul style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<li style="margin-top: 0pt; margin-bottom: 0pt;
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initial initial">
<span style="margin-top: 0pt; margin-bottom: 0pt;
background-position: initial initial; background-repeat:
initial initial">make movie</span></li>
</ul>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
margin-bottom: 0pt; background-position: initial initial;
background-repeat: initial initial">
<span style="margin-top: 0pt; margin-bottom: 0pt;
background-position: initial initial; background-repeat:
initial initial">movie record size 1000,1000</span></p>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<span style="margin-top: 0pt; margin-bottom: 0pt;
background-position: initial initial; background-repeat:
initial initial">coordset #3</span></p>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<span style="margin-top: 0pt; margin-bottom: 0pt;
background-position: initial initial; background-repeat:
initial initial">wait 100</span></p>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
margin-bottom: 0pt; background-position: initial initial;
background-repeat: initial initial">
<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>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
margin-bottom: 0pt; background-position: initial initial;
background-repeat: initial initial">
<br>
</p>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
margin-bottom: 0pt; background-position: initial initial;
background-repeat: initial initial">
<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>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
margin-bottom: 0pt; background-position: initial initial;
background-repeat: initial initial">
<br>
</p>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<span style="margin-top: 0pt; margin-bottom: 0pt;
background-position: initial initial; background-repeat:
initial initial">Thanks,</span></p>
<p style="color: rgb(14, 16, 26); margin-top: 0pt;
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background-repeat: initial initial">
<span style="margin-top: 0pt; margin-bottom: 0pt;
background-position: initial initial; background-repeat:
initial initial">Nandish</span></p>
<br>
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<br>
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