[chimerax-users] alphafold contacts output file

[Tom Goddard]

Hi Philip,

  The alphafold contacts code as it is currently written finds the pairs of close residues but does not remember which atoms were the closest so it can't easily output the closest atoms between a pair of residues.  But the ChimeraX contacts command or tool is actually intended to find contacting residues and uses more sophisticated criteria that take into account the van der Waals radii of the atoms.

	https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html <https://www.cgl.ucsf.edu/chimerax/docs/user/tools/clashes.html>
        https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/clashes.html>

  Confidence in whether two proteins really make a biological contact in for example a crystal structure where the proteins may must be touching due to crystal packing is usually judge by the total area of contact residues, not by how close individual residues are to each other.  The ChimeraX buried surface area calculation calculates how much surface is in contact (square Angstroms).

	measure buriedarea /A with /B
	> Buried area between /A and /B = 484.71

  To judge if an AlphaFold prediction of a protein-protein interface is correct I suggest looking at both the buried surface area and also the the AlphaFold PAE values between residue pairs at the interface.

	Tom


> On Oct 4, 2022, at 10:08 AM, McClean, Phillip <phillip.mcclean at ndsu.edu> wrote:
> 
> Hi Tom,
> 
> Thanks.  Found it on the desktop.
> 
> A follow-up Chimerax question (hopefully it shouldn't be a different thread).  Is it possible to list the atoms that are in close contact in the output file.
> 
> And a general newbie question.  You choose a distance of 3 as the default cutoff.  In the computational protein-protein modeling world, is this considered good evidence of contact between two proteins.  The reason I ask is that I have discovered wild type and mutant alleles of a MYB protein which were modeled with Alphafold  multimer along with its functional beta helix-loop-helix protein partner.  If I see changes in distances might that suggest changes in interaction capacity of any sort?
> 
> Phil McClean
> From: Tom Goddard <goddard at sonic.net>
> Sent: Tuesday, October 4, 2022 11:57 AM
> To: McClean, Phillip <phillip.mcclean at ndsu.edu>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] alphafold contacts output file
>  
> Hi Phil,
> 
>   If you start ChimeraX by clicking an icon then it puts files on your desktop.  If you start it from a shell (for example on Linux) it will put the files in the directory you started in.  To find the directory ChimeraX is currently in use the ChimeraX pwd command
> 
> pwd <applewebdata://91B35BD3-59DE-4B72-AC13-CF0B634EFF2F>Current working directory is: /Users/goddard/Desktop
> 
> To change the directory ChimeraX is currently in use the cd command
> 
> cd ~/Documents <applewebdata://91B35BD3-59DE-4B72-AC13-CF0B634EFF2F>Current working directory is: /Users/goddard/Documents
> 
> Lastly you can give a full path to the output file in your command
> 
> alphafold contacts /B to /C output /Users/goddard/contact_pae.txt
> 
> or
> 
> alphafold contacts /B to /C output ~/contact_pae.txt
> 
> where "~" means your user account home directory.
> 
>    Tom
> 
>> On Oct 4, 2022, at 9:21 AM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu <mailto:chimerax-users at cgl.ucsf.edu>> wrote:
>> 
>> Hi Everyone-
>> 
>> I used the following command to obtain a file with the contacts between two chains:
>> 
>> alphafold contacts /B to /C output contact_pae.txt
>> I cannot seem to find where the output file is located.
>> 
>> Thanks for any help.
>> 
>> Phil McClean
>> _______________________________________________
>> ChimeraX-users mailing list
>> ChimeraX-users at cgl.ucsf.edu <mailto:ChimeraX-users at cgl.ucsf.edu>
>> Manage subscription:
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://www.rbvi.ucsf.edu/pipermail/chimerax-users/attachments/20221004/168143aa/attachment.html>