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