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 <cxcmd:pwd>Current working directory is: /Users/goddard/Desktop To change the directory ChimeraX is currently in use the cd command cd ~/Documents <cxcmd:cd /Users/goddard/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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>