Do you knwo how to use Rosetta to calculate the cross correlation value of crystal structure with EM map?
There is a program 'density_tools' that will do this:
$ROSETTA/bin/density_tools.linuxgccrelease -s infile.pdb -mapfile map.mrc -mapreso 3.0 -nresbins 50 -cryoem_scatterers -verbose -mask_resolution 10
This will give you a full model/map FSC curve. Change the input and map (and map resolution) accordingly.
If you just want integrated FSC over some resolution range:
$ROSETTA/bin/density_tools.linuxgccrelease -s infile.pdb -mapfile map.mrc -mapreso 3.0 -nresbins 20 -cryoem_scatterers -mask_resolution 10 -hires 3 -lowres 10
Thank you, Frank.
I have seen it needs the mask_resolution option in your script. Does this tool generate a mask around pdb file and then calculate the CC value using that mask? Since I want to use the CC value to calibrate the microscope maginification, I think it is not good to use a mask for that purpose.