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

[Tom Goddard]

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> 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> 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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