[chimerax-users] alphafold contacts output file

[McClean, Phillip]

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
Current working directory is: /Users/goddard/Desktop

To change the directory ChimeraX is currently in use the cd command

cd ~/Documents
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
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