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Hi Phil,</div>
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<br>
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Another solution would be to use <a href="https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html" title="https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html">
MatchMaker</a> instead. Instead of the command you tried, use:</div>
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mmaker #1:11-323 to #2:24-336</div>
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In my experience, MatchMaker is quite powerful.</div>
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<br>
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Best,</div>
<div style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 12pt; color: rgb(0, 0, 0); background-color: rgb(255, 255, 255);" class="elementToProof">
Harper </div>
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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 Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
<b>Sent:</b> Monday, July 18, 2022 5:33 PM<br>
<b>To:</b> McClean, Phillip <phillip.mcclean@ndsu.edu><br>
<b>Cc:</b> chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Align command; designating the positions to align</font>
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Hi Phil,<br>
Your syntax is fine if you really meant to specify all atoms of the residues. Most likely reasons for the error are:<br>
<br>
(1) the residue types are not identical, so they contain different numbers of atoms (e.g. tryptophan has many more atoms than alanine)<br>
(2) one structure or the other is missing some residues from the coordinates (e.g. a flexible loop was not resolved from density)<br>
(3) one structure or the other has multiple chains so you are getting residues with those numbers from more than one chain (e.g. chain A has residues 11-323 but so does chain B)<br>
<br>
Another possible problem is that there is no underscore in the "toAtoms" option keyword. You can truncate it to "to" if you like.<br>
<br>
<<a href=""></a>https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/align.html__;!!KGKeukY!xCbiexKkpg7JPT323Wwlpw5TX3YDnnS921fjgr03zjvBl0Gp3g9AO0jDyorUMvvDg8gxubpM4mHneWhdi7byEnMoUqUZD_ik7EI$ ><br>
<br>
Assuming it is the first one, the solution is to specify matching only backbone atoms, or only alpha-carbons. Whichever you would like the RMSD to reflect. You would use an @ symbol to specify atom names. So it may be something like<br>
<br>
align #1:11-323@n,ca,c,o to #2:24-336@n,ca,c,o<br>
<br>
...for all backbone atoms, or for alpha-carbons only:<br>
<br>
align #1:11-323@ca to #2:24-336@ca<br>
<br>
<<a href=""></a>https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html__;!!KGKeukY!xCbiexKkpg7JPT323Wwlpw5TX3YDnnS921fjgr03zjvBl0Gp3g9AO0jDyorUMvvDg8gxubpM4mHneWhdi7byEnMoUqUZzPSqGIk$ ><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Jul 18, 2022, at 2:22 PM, McClean, Phillip via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi,<br>
> <br>
> I have been trying to properly code the align command. I would like to use the command to determine the RMSD value between corresponding sections of two highly homologous proteins. Here are the details:<br>
> <br>
> Model 1 is to be aligned to Model 2; each model only has one chain<br>
> Model 1 positions (residues=amino acids) 11-323<br>
> Model 2 positions ( residues=amino acids) 24-336<br>
> <br>
> When I pair each of the amino acids that are being aligned, everyone of the pairs has the same number of atoms.<br>
> <br>
> Here is what I thought would work:<br>
> <br>
> align #1:11-323 to_atoms #2:24-336<br>
> <br>
> Here is the error message:<br>
> <br>
> Unequal number of atoms to pair, 2483 to 2371<br>
> <br>
> I am still trying to understand the nomenclature for understanding residues and atoms.<br>
> <br>
> Thanks for any help you can provide.<br>
> <br>
> Phil McClean<br>
<br>
<br>
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