Volume scale of reference

Dear all,

I’m using molmap of chimerax to generate a reference map from pdb.
I was wondering that whether the black/white values range of the reference map will influence the template matching result?

Tanks and cheers,

Hi @yanhezhao,

If you are planning on using the reference map for template picking (for e.g. by importing it into CryoSPARC, running the Create Templates job, and then running the Template Picker), then the grayscale range of the map should not affect the quality of the subsequent particle picking. It would be wise to low-pass filter the reference (e.g. via the Volume Tools job) prior to creating templates, in order to reduce potential overfitting from the “Einstein from noise” phenomenon.

If you are planning using the reference map as an initial model for refinement, then the grayscale also won’t affect the results because the map is re-scaled to match the particles at the start of the job. However, we wouldn’t recommend this approach; there is significant potential for overfitting, and refinement can be quite sensitive to the initial model.



Hi Michael,

Thanks a lot for clarifying. Yes, I did try different grayscale of reference map, as you said it shown no affect on picking.

Thanks you so much and cheers,