[chimerax-users] alphafold contacts output file

[Tom Goddard]

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 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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