[Chimera-users] Help Generating Spheres

Flaherty, Daniel P dflaher at purdue.edu
Thu Aug 6 19:38:31 PDT 2015


I’m teaching myself to perform molecular modeling and docking using your tutorials.   I am trying to prepare a protein for a vHTS and I have run into a snag during the sphere generation tutorial (http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm).

In the section where it says,"To generate the spheres, simply use the command "sphgen"  in the same folder that contains the INSPH and the rec.ms files. The output will be two files: rec.sph<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/rec.sph>, which contains the spheres in clusters, and OUTSPH<http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/OUTSPH>, which contains general information about the calculation.”

I am getting an error that says Unrecognized command: “sphgen”.   I downloaded the INSPH text file but I have no idea what to do with it.  I don’t know what “folder” the tutorial refers to when it says,”use the command ‘sphgen’ in the same folder that contains the INSPH and rec.ms files."

Any help would be greatly appreciated!


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