cross correlation calculation

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    • April 17, 2016 at 2:11 am #2409
      Anonymous

        Dear all:

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

      • April 29, 2016 at 12:18 am #11547
        Anonymous

          Hello,

          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

          -Frank

        • May 5, 2016 at 6:26 am #11563
          Anonymous

            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.

            Jingwei

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