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Steven,</div>
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I can't answer the second part of your question, but the RMSD can be obtained from the "run" function in python:</div>
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```<br>
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from chimerax.core.commands import run</div>
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value = run(session, "rmsd #1 to #2")</div>
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if value > 2:</div>
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# do stuff<br>
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```</div>
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Best,</div>
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Tony<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Steven Truong via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, October 12, 2021 3:39 PM<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> [chimerax-users] Use values printed from Log inside a script (e.g. RMSD)</font>
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<div class="PlainText">[EXTERNAL SENDER - PROCEED CAUTIOUSLY]<br>
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<br>
Dear ChimeraX Admins,<br>
<br>
I was hoping to use the “rmsd” command in ChimeraX to measure distances between models within a .py script.<br>
<br>
Is there a way to use the output of “rmsd” (or generally any other output in Log) within the script? For example, if rmsd > 2 Angstroms, then do X.<br>
<br>
Ultimately, I am attempting to align chains between models. Because my protein is asymmetric, chain A on Model #1 might actually be chain B on Model #2. I was hoping to use “rmsd” to map one chain to the other. Is it a better idea to do this in another program
and re-write chain IDs in the .PDB file? If so, what other program would be better at making RMSD calculations between .PDB chains?<br>
<br>
Thank you,<br>
Steven Truong<br>
Cambridge University<br>
<br>
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