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@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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