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<div>Dear ChimeraX users support, </div>
<div dir="ltr">Thanks for making AlphaFold such accessible and user <span>friendly tool that has added a great deal to my protein-protein investigations. </span></div>
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<div dir="ltr"><span>I have modelled a number of protein complexes a long while ago effortlessly. However, i need to get the PAE for the best model only, so I managed to know which model is the best because from file name but the pae.json file does not. <span></span></span></div>
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<div dir="ltr"><span>Just I am wondering <span>if there is a way to know which json file is associated with the best model? </span></span></div>
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<div dir="ltr"><span><span>Thanks a lot. </span></span></div>
<div dir="ltr"><span><span>Asmahan </span></span></div>
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</span></div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Asmahan Alghamdi <stxamalg@exmail.nottingham.ac.uk><br>
<b>Sent:</b> Thursday, June 23, 2022 9:39:46 AM<br>
<b>To:</b> Tom Goddard <goddard@sonic.net>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)</font>
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<div dir="ltr">Thank you very much, I will try that and see how it goes. </div>
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<div dir="ltr">your help is much appreciated.</div>
<div dir="ltr">Asmahan Alghamdi </div>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Thursday, June 23, 2022 12:52:50 AM<br>
<b>To:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>; Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Cc:</b> Asmahan Alghamdi <stxamalg@exmail.nottingham.ac.uk><br>
<b>Subject:</b> Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)</font>
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<div class="x_PlainText">Hi Asmahan,<br>
<br>
I added an outputFile option to the "alphafold contacts" command so the pairs of close residues and their PAE value can be written to a file. This will be in tomorrow's ChimeraX daily build.<br>
<br>
alphafold contacts /B to /C output contact_pae.txt<br>
<br>
and the output_pae.txt file looks like<br>
<br>
/B:24 /C:30 4.30<br>
/B:56 /C:9 9.84<br>
/B:68 /C:32 1.48<br>
...<br>
<br>
with chain identifier and residue number for both residues and their PAE value.<br>
<br>
Elaine is right that the PAE values are in a file produced by AlphaFold. For ChimeraX AlphaFold predictions using Google Colab the file is JSON format (text) like<br>
<br>
~/Downloads/ChimeraX/AlphaFold/prediction_20/best_model_pae.json<br>
<br>
If you run your own installation of AlphaFold with multimer or monomer_ptm presets the PAE data is in Python pkl format (binary) like<br>
<br>
alphafold_output/result_model_1_multimer_v2_pred_0.pkl<br>
<br>
Each of these files have a matrix of all residue by all residue PAE values. It is not too convenient to get the values for specific residues out of such a file unless you write some code. That is why I made ChimeraX do it for you.<br>
<br>
Tom<br>
<br>
> On Jun 22, 2022, at 1:43 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Dear Asmahan Alghamdi ,<br>
> I am guessing you are talking about the AlphaFold PAE values. These are output by the AlphaFold calculation into a file. What you see as a plot using ChimeraX was already read from that file. So you don't need to export it, you just need to find the file
that already exists.<br>
> <br>
> I am not sure where this file is stored, or whether it is in some "temp" location. We will get back to you on that.<br>
> <br>
> I should also clarify that a PAE value by itself is not a measure of how likely the residues are in contact. It is the predicted error in the relationship between the two residues in the Alphafold-predicted structure, where some pairs of residues are close
together like a contact, but many more are far apart and not in contact. Although the "alphafold contacts" command does draw lines between residues that are close together based on a cutoff value, the presence of a line does not mean a contact is predicted
with high confidence unless its coloring also shows a favorable PAE value.<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>
> <br>
>> On Jun 22, 2022, at 1:21 PM, Asmahan Alghamdi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
>> <br>
>> Dear Chimerax team, <br>
>> <br>
>> Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations.
<br>
>> <br>
>> Recently I succeeded in using version 1.5 to determine contacts and the correlated confidence but exporting that list of contact not clear to me yet although searched within software guide and tutorials available online.
<br>
>> <br>
>> Your help would be much appreciated in this respect. <br>
>> <br>
>> Thanks in advance<br>
>> Asmahan Alghamdi <br>
>> The university of Nottingham <br>
> <br>
> <br>
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> <br>
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