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

[Elaine Meng]

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