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<div>That is very helpful. Now I can compare the suggested contact residues from PAE file of the best model with those from correspondent resolved complex structure. </div>
<div dir="ltr">Thank you very much. </div>
<div dir="ltr">Asmahan </div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Monday, September 12, 2022 9:45:32 PM<br>
<b>To:</b> Asmahan Alghamdi <stxamalg@exmail.nottingham.ac.uk><br>
<b>Cc:</b> ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject:</b> Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)</font>
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<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Asmahan,
<div class=""><br class="">
</div>
<div class=""> Ok, probably you used ChimeraX 1.3 since 1.4 was not released in December 2021. So of course Model_1_multimer_pae.json goes with Model_1_multimer_unrelaxed.pdb. And Model_5_multimer_relaxed.pdb is the energy minimized version of Model_5_multimer_unrelaxed.pdb
and in that older ChimeraX it only energy minimized the best scoring model so model 5 is the best scoring one. The best_model.pdb file is a copy of Model_5_multimer_relaxed.pdb.</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
<div class=""><br class="">
</div>
<div class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Sep 12, 2022, at 1:07 PM, Asmahan Alghamdi <<a href="mailto:Asmahan.Alghamdi@nottingham.ac.uk" class="">Asmahan.Alghamdi@nottingham.ac.uk</a>> wrote:</div>
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<div dir="ltr" class="">Hi Tom,</div>
<div dir="ltr" class="">Thank you very much for your time and help. </div>
<div dir="ltr" class=""><br class="">
</div>
<div dir="ltr" class="">I used ChimeraX 1.4 December 2021 on my laptop. The type of files I have got are as follows: </div>
<div dir="ltr" class=""><br class="">
</div>
<div dir="ltr" class="">Best model file , then three files for each model except model 5 in this particular prediction</div>
<div dir="ltr" class=""><br class="">
</div>
<div dir="ltr" class="">Model_1_multimer_pae.json</div>
<div dir="ltr" class="">Model_1_multimer score</div>
<div dir="ltr" class="">Model_1_multimer_unrelaxed </div>
<div dir="ltr" class=""><br class="">
</div>
<div dir="ltr" class="">The same for model2,3,4</div>
<div dir="ltr" class=""><br class="">
</div>
<div dir="ltr" class="">But 5 with extra file that is: model_5_relaxed </div>
<div dir="ltr" class=""><br class="">
</div>
<div dir="ltr" class="">After that, a list of sequence files </div>
<div dir="ltr" class=""><br class="">
</div>
<div dir="ltr" class="">Best regards </div>
<div dir="ltr" class="">Asmahan </div>
</div>
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<div id="x_divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b> Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class="">
<b class="">Sent:</b> Monday, September 12, 2022 8:03:22 PM<br class="">
<b class="">To:</b> Asmahan Alghamdi <<a href="mailto:stxamalg@exmail.nottingham.ac.uk" class="">stxamalg@exmail.nottingham.ac.uk</a>><br class="">
<b class="">Cc:</b> ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class="">
<b class="">Subject:</b> Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)</font>
<div class=""> </div>
</div>
<div class="" style="word-wrap:break-word; line-break:after-white-space">Hi Asmahan,
<div class=""><br class="">
</div>
<div class=""> I'm not sure how you ran your AlphaFold prediction. Currently ChimeraX AlphaFold predictions creates JSON PAE files that match the 5 predicted models</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">af111_unrelaxed_rank_1_model_4.pdb</div>
<div class="">af111_unrelaxed_rank_1_model_4_scores.json</div>
<div class="">af111_unrelaxed_rank_2_model_5.pdb</div>
<div class="">af111_unrelaxed_rank_2_model_5_scores.json</div>
<div class="">af111_unrelaxed_rank_3_model_3.pdb</div>
<div class="">af111_unrelaxed_rank_3_model_3_scores.json</div>
<div class="">af111_unrelaxed_rank_4_model_2.pdb</div>
<div class="">af111_unrelaxed_rank_4_model_2_scores.json</div>
<div class="">af111_unrelaxed_rank_5_model_1.pdb</div>
<div class="">af111_unrelaxed_rank_5_model_1_scores.json</div>
</div>
<div class=""><br class="">
</div>
<div class="">The file names have both the scoring order (rank 1 best, rank 5 worst). If you ran AlphaFold on your local machine it might put out</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">relaxed_model_1_multimer.pdb</div>
<div class="">relaxed_model_2_multimer.pdb</div>
<div class="">relaxed_model_3_multimer.pdb</div>
<div class="">relaxed_model_4_multimer.pdb</div>
<div class="">relaxed_model_5_multimer.pdb</div>
<div class="">result_model_1_multimer.pkl</div>
<div class="">result_model_2_multimer.pkl</div>
<div class="">result_model_3_multimer.pkl</div>
<div class="">result_model_4_multimer.pkl</div>
<div class="">result_model_5_multimer.pkl</div>
</div>
<div class=""><br class="">
</div>
<div class="">where the .pkl files contain the PAE data. These are not in score ranked order but you can find the score ranked order from another file AlphaFold writes</div>
<div class=""><br class="">
</div>
<div class="">ranking_debug.json</div>
<div class=""><br class="">
</div>
<div class="">There are other ways to run AlphaFold that give different output files. You'd have to show your list of output files to advise further.</div>
<div class=""><br class="">
</div>
<div class=""><span class="x_x_Apple-tab-span" style="white-space:pre"></span>Tom</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On Sep 12, 2022, at 2:37 AM, Asmahan Alghamdi via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:</div>
<br class="x_x_Apple-interchange-newline">
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<div class="">
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<div class="">Dear ChimeraX users support, </div>
<div dir="ltr" class="">Thanks for making AlphaFold such accessible and user <span class="">friendly tool that has added a great deal to my protein-protein investigations. </span></div>
<div dir="ltr" class=""><span class=""><br class="">
</span></div>
<div dir="ltr" class=""><span class="">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 class=""></span></span></div>
<div dir="ltr" class=""><span class=""><br class="">
</span></div>
<div dir="ltr" class=""><span class="">Just I am wondering <span class="">if there is a way to know which json file is associated with the best model? </span></span></div>
<div dir="ltr" class=""><span class=""><span class=""><br class="">
</span></span></div>
<div dir="ltr" class=""><span class=""><span class="">Thanks a lot. </span></span></div>
<div dir="ltr" class=""><span class=""><span class="">Asmahan </span></span></div>
<div dir="ltr" class=""><span class=""><br class="">
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<div id="x_x_divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b> Asmahan Alghamdi <<a href="mailto:stxamalg@exmail.nottingham.ac.uk" class="">stxamalg@exmail.nottingham.ac.uk</a>><br class="">
<b class="">Sent:</b> Thursday, June 23, 2022 9:39:46 AM<br class="">
<b class="">To:</b> Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>>; ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>>; Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class="">
<b class="">Subject:</b> Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)</font>
<div class=""> </div>
</div>
<div class="">
<div class="">
<div class="">
<div dir="ltr" class="">Thank you very much, I will try that and see how it goes. </div>
<div dir="ltr" class=""><br class="">
</div>
<div dir="ltr" class="">your help is much appreciated.</div>
<div dir="ltr" class="">Asmahan Alghamdi </div>
<div dir="ltr" class=""><br class="">
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<div id="x_x_x_divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b> Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class="">
<b class="">Sent:</b> Thursday, June 23, 2022 12:52:50 AM<br class="">
<b class="">To:</b> ChimeraX Users Help <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>>; Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>><br class="">
<b class="">Cc:</b> Asmahan Alghamdi <<a href="mailto:stxamalg@exmail.nottingham.ac.uk" class="">stxamalg@exmail.nottingham.ac.uk</a>><br class="">
<b class="">Subject:</b> Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)</font>
<div class=""> </div>
</div>
<div class="x_x_x_BodyFragment"><font size="2" class=""><span class="" style="font-size:11pt">
<div class="x_x_x_PlainText">Hi Asmahan,<br class="">
<br class="">
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 class="">
<br class="">
alphafold contacts /B to /C output contact_pae.txt<br class="">
<br class="">
and the output_pae.txt file looks like<br class="">
<br class="">
/B:24 /C:30 4.30<br class="">
/B:56 /C:9 9.84<br class="">
/B:68 /C:32 1.48<br class="">
...<br class="">
<br class="">
with chain identifier and residue number for both residues and their PAE value.<br class="">
<br class="">
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 class="">
<br class="">
~/Downloads/ChimeraX/AlphaFold/prediction_20/best_model_pae.json<br class="">
<br class="">
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 class="">
<br class="">
alphafold_output/result_model_1_multimer_v2_pred_0.pkl<br class="">
<br class="">
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 class="">
<br class="">
Tom<br class="">
<br class="">
> On Jun 22, 2022, at 1:43 PM, Elaine Meng via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">
> <br class="">
> Dear Asmahan Alghamdi ,<br class="">
> 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 class="">
> <br class="">
> 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 class="">
> <br class="">
> 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 class="">
> <br class="">
> I hope this helps,<br class="">
> Elaine<br class="">
> -----<br class="">
> Elaine C. Meng, Ph.D. <br class="">
> UCSF Chimera(X) team<br class="">
> Department of Pharmaceutical Chemistry<br class="">
> University of California, San Francisco<br class="">
> <br class="">
> <br class="">
>> On Jun 22, 2022, at 1:21 PM, Asmahan Alghamdi via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>> wrote:<br class="">
>> <br class="">
>> Dear Chimerax team, <br class="">
>> <br class="">
>> Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations.
<br class="">
>> <br class="">
>> 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 class="">
>> <br class="">
>> Your help would be much appreciated in this respect. <br class="">
>> <br class="">
>> Thanks in advance<br class="">
>> Asmahan Alghamdi <br class="">
>> The university of Nottingham <br class="">
> <br class="">
> <br class="">
> _______________________________________________<br class="">
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