Hi Thu Nguyen, It is better to use the "Report Bug" button as shown in your screenshot instead of sending email to chimerax-users. However, this time I already created the bug report for you, ticket https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17922 Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jun 5, 2025, at 11:13 AM, Thu Nguyen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I am trying to calculate the Q-score of this density map and structure pair using the Q-Score plugin in ChimeraX and save the score to the output file. I loaded the 2 files to ChimeraX and used this command "qscore #2 toVolume #1 useGui false pointsPerShell 8 shellRadiusStep 0.100 maxShellRadius 2.00 referenceGaussianSigma 0.60 logDetails false outputFile /Desktop/q_score.txt" However, the output file is empty and I got the error message in ChimeraX. When I removed the outputFile option, it worked as normal and gave me the average score of .32. Do you know why it happened like this and what I should do to fix it? Thank you very much.

Best regards, Thu

<4427_6i7o_AY_fitted.cif><4427_6i7o_AY.mrc><Screenshot 2025-06-05 at 2.05.42 PM.png>