[chimerax-users] Export list of contacts (AlphaFold PAE?)

Tom Goddard goddard at sonic.net
Mon Sep 12 13:45:32 PDT 2022 

Hi Asmahan,

  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.

	Tom


> On Sep 12, 2022, at 1:07 PM, Asmahan Alghamdi <Asmahan.Alghamdi at nottingham.ac.uk> wrote:
> 
> Hi Tom,
> Thank you very much for your time and help. 
> 
> I used ChimeraX 1.4 December 2021 on my laptop. The type of files I have got are as follows: 
> 
> Best model file , then three files for each model except model 5 in this particular prediction
> 
> Model_1_multimer_pae.json
> Model_1_multimer score
> Model_1_multimer_unrelaxed 
> 
> The same for model2,3,4
> 
> But 5 with extra file that is: model_5_relaxed 
> 
> After that, a list of sequence files 
> 
> Best regards 
> Asmahan 
> 
> Get Outlook for iOS <https://aka.ms/o0ukef>
> From: Tom Goddard <goddard at sonic.net>
> Sent: Monday, September 12, 2022 8:03:22 PM
> To: Asmahan Alghamdi <stxamalg at exmail.nottingham.ac.uk>
> Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)
>  
> Hi Asmahan,
> 
>   I'm not sure how you ran your AlphaFold prediction.  Currently ChimeraX AlphaFold predictions creates JSON PAE files that match the 5 predicted models
> 
> af111_unrelaxed_rank_1_model_4.pdb
> af111_unrelaxed_rank_1_model_4_scores.json
> af111_unrelaxed_rank_2_model_5.pdb
> af111_unrelaxed_rank_2_model_5_scores.json
> af111_unrelaxed_rank_3_model_3.pdb
> af111_unrelaxed_rank_3_model_3_scores.json
> af111_unrelaxed_rank_4_model_2.pdb
> af111_unrelaxed_rank_4_model_2_scores.json
> af111_unrelaxed_rank_5_model_1.pdb
> af111_unrelaxed_rank_5_model_1_scores.json
> 
> 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
> 
> relaxed_model_1_multimer.pdb
> relaxed_model_2_multimer.pdb
> relaxed_model_3_multimer.pdb
> relaxed_model_4_multimer.pdb
> relaxed_model_5_multimer.pdb
> result_model_1_multimer.pkl
> result_model_2_multimer.pkl
> result_model_3_multimer.pkl
> result_model_4_multimer.pkl
> result_model_5_multimer.pkl
> 
> 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
> 
> ranking_debug.json
> 
> 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.
> 
> Tom
> 
> 
>> On Sep 12, 2022, at 2:37 AM, Asmahan Alghamdi via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> 
>> 
>> Dear ChimeraX users support, 
>> Thanks for making AlphaFold such accessible and user friendly tool that has added a great deal to my protein-protein investigations. 
>> 
>> 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. 
>> 
>> Just I am wondering if there is a way to know which json file is associated with the best model? 
>> 
>> Thanks a lot. 
>> Asmahan 
>> 
>> Get Outlook for iOS <https://aka.ms/o0ukef>
>> From: Asmahan Alghamdi <stxamalg at exmail.nottingham.ac.uk <mailto:stxamalg at exmail.nottingham.ac.uk>>
>> Sent: Thursday, June 23, 2022 9:39:46 AM
>> To: Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>; ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>; Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
>> Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)
>>  
>> Thank you very much, I will try that and see how it goes. 
>> 
>> your help is much appreciated.
>> Asmahan Alghamdi  
>> 
>> 
>> Get Outlook for iOS <https://aka.ms/o0ukef>
>> From: Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>>
>> Sent: Thursday, June 23, 2022 12:52:50 AM
>> To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>>; Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
>> Cc: Asmahan Alghamdi <stxamalg at exmail.nottingham.ac.uk <mailto:stxamalg at exmail.nottingham.ac.uk>>
>> Subject: Re: [chimerax-users] Export list of contacts (AlphaFold PAE?)
>>  
>> Hi Asmahan,
>> 
>>   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.
>> 
>>         alphafold contacts /B to /C output contact_pae.txt
>> 
>> and the output_pae.txt file looks like
>> 
>>         /B:24 /C:30 4.30
>>         /B:56 /C:9 9.84
>>         /B:68 /C:32 1.48
>>         ...
>> 
>> with chain identifier and residue number for both residues and their PAE value.
>> 
>>   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
>> 
>>         ~/Downloads/ChimeraX/AlphaFold/prediction_20/best_model_pae.json
>> 
>> If you run your own installation of AlphaFold with multimer or monomer_ptm presets the PAE data is in Python pkl format (binary) like
>> 
>>         alphafold_output/result_model_1_multimer_v2_pred_0.pkl
>> 
>> 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.
>> 
>>         Tom
>> 
>> > On Jun 22, 2022, at 1:43 PM, Elaine Meng via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> > 
>> > Dear Asmahan Alghamdi ,
>> > 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.
>> > 
>> > 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.
>> > 
>> > 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.
>> > 
>> > I hope this helps,
>> > Elaine
>> > -----
>> > Elaine C. Meng, Ph.D.                       
>> > UCSF Chimera(X) team
>> > Department of Pharmaceutical Chemistry
>> > University of California, San Francisco
>> > 
>> > 
>> >> On Jun 22, 2022, at 1:21 PM, Asmahan Alghamdi via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> >> 
>> >> Dear Chimerax team, 
>> >> 
>> >> Thanks a lot for the extremely useful software that has been helping a great deal in improving my protein complex investigations. 
>> >> 
>> >> 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. 
>> >> 
>> >> Your help would be much appreciated in this respect.  
>> >> 
>> >> Thanks in advance
>> >> Asmahan Alghamdi 
>> >> The university of Nottingham 
>> > 
>> > 
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