If you are running Chimera in "nogui" mode from a terminal, then output that would normally go to the Log tool goes to the terminal instead. So you should be able to save the matchmaker results by redirecting the ChimeraX output to a file.

However, if you are run() in a Python script to run matchmaker, then you should know that the return value from run() contains all the pertinent information and is much easier to deal with than parsing the log output. The contents of the return value is described in this previous mailing list message: [chimerax-users] capture reply from run(session, command).

On Mar 14, 2022, at 11:11 AM, Steven Truong via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX admins,

I am using matchmaker (mmaker) since the RMSD calculations done using the function have been very useful. However, I’m currently having some trouble outputting these values. At first, I tried to use matchmaker in a .PY script and then output these values via “log save”. Unfortunately, I haven’t been able to get this to work because whenever I try to do “log save” in a script (in terminal/command line), I get “no log tool to save”. Is there a way to “log save” if running a .PY script in a command line? Or is there a simpler way to get the values I need from matchmaker?

Thank you for your help,

Steven Truong

sdt45@cam.ac.uk

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