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Thx Elaine for the reassurance about the contacts output. I will send me questions to via the question portal next time.</div>
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Phil</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Tuesday, September 27, 2022 5:35 PM<br>
<b>To:</b> McClean, Phillip <phillip.mcclean@ndsu.edu><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: alphafold contacts output</font>
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> On Sep 27, 2022, at 1:59 PM, McClean, Phillip <phillip.mcclean@ndsu.edu> wrote:<br>
> <br>
> Hi Elaine, <br>
> <br>
> I am using output data from alphafold2 multimer as provided by Colabfold. Following the video (<a href="https://www.youtube.com/watch?v=TMcjEecFHaI&t=6s">https://www.youtube.com/watch?v=TMcjEecFHaI&t=6s</a>), I use the following command:<br>
> <br>
> <br>
> alphafold contacts /b to /c distance 8<br>
> <br>
> For my complex, the links at the distance are all blue (good results). What is confusing is that the distance of some of the contacts are greater than 8 angstroms. Those distances are between backbone carbon atoms, I assume. The fact that the command asks
for amino acid pairs that are less than 8 angstroms apart suggest that other atoms than those in the backbone are less than 8 angstroms. Is my conclusion correct.<br>
> <br>
> Thanks as always for the advise.<br>
> <br>
> Phil<br>
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Hi Phil,<br>
Yes, your conclusion is correct - the distance cutoff applies to any atom in the residue within any atom in the other residue, whereas the pseudobond is drawn between alpha-carbons, as mentioned here:<br>
<br>
<<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts">https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts</a>><br>
<br>
We generally recommend sending questions to chimerax-users@cgl.ucsf.edu (CC'd here) since many heads are better than my one, unless you are including some data that needs to remain private.<br>
<br>
Best,<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>
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