Dear Daniel, The error you are getting only says that the sphgen program is not in your $PATH and therefore the shell cannot find the executable to run. Make sure you have installed DOCK6, which is not bundled with Chimera. You need to apply for the DOCK6 license (free for academia) and the "sphgen" program will be bundled with it. Apply here: http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html After you have made sure DOCK6 is properly installed by following the instructions below, you can follow all the tutorials available online. http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation Best, Matej ------------------------------------------------------ Dr. Matej Repic Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Chemistry and Biochemistry SB - ISIC – LCBC BCH 4108 CH - 1015 Lausanne ------------------------------------------------------ From: <chimera-users-bounces@cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of "Flaherty, Daniel P" <dflaher@purdue.edu<mailto:dflaher@purdue.edu>> Date: Friday, August 7, 2015 at 04:38 To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: [Chimera-users] Help Generating Spheres Hello, 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_s...). 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! Thanks, Dan