Dear Eric,<div><br></div><div>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.</div><div><br></div><div>Thanks for getting back to me.</div><div><br></div><div>Kind Regards<br><br>On Friday, May 13, 2022, Eric Pettersen <<a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">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?<br>
<br>
—Eric<br>
<br>
> On May 10, 2022, at 4:34 PM, Reeki Emrizal via Chimera-users <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>> wrote:<br>
> <br>
> Hi<br>
> <br>
> 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.<br>
> <br>
> 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?<br>
> <br>
> I found previous post with similar issue that use:<br>
> <br>
> from chimera.tkgui import saveReplyLog<br>
> saveReplyLog(path)<br>
> <br>
> The solution does not work for me though as the text file is empty even though there is content in the reply log.<br>
> <br>
> Kind Regards<br>
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</blockquote></div>