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cross correlation calculation

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cross correlation calculation

Dear all:

Do you knwo how to use Rosetta to calculate the cross correlation value of crystal structure with EM map?

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Sat, 2016-04-16 19:11
jingwei xu


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


Thu, 2016-04-28 17:18

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.

Best wishes.


Wed, 2016-05-04 23:26
jingwei xu