Dear Eric, Actually I have solved the issue. I believe the — no status option that I have used suppress the output to the terminal. Removing that option, I can see the rmsd value printed in the terminal. Thanks for getting back to me. Kind Regards On Friday, May 13, 2022, Eric Pettersen <pett@cgl.ucsf.edu> wrote:

If you are in nogui mode, log output should simply go to the terminal that you are running Chimera from, and which you can redirect to a file. Is that not what’s happening?

—Eric

...

On May 10, 2022, at 4:34 PM, Reeki Emrizal via Chimera-users < chimera-users@cgl.ucsf.edu> wrote:

Hi

I working on an automated python script to calculate the rmsd between two molecules using rmsd command. I'm using --nogui when running the script. The standard output did not show the rmsd value.

When using the chimera gui, I noticed that the rmsd value is shown in the reply log. Is there a way I could save the content of the reply log through python script?

I found previous post with similar issue that use:

from chimera.tkgui import saveReplyLog saveReplyLog(path)

The solution does not work for me though as the text file is empty even though there is content in the reply log.

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