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<div>Dear Daniel,</div>
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<div>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:</div>
<div><a href="http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html">http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html</a></div>
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<div>After you have made sure DOCK6 is properly installed by following the instructions below, you can follow all the tutorials available online.</div>
<div><a href="http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation">http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Installation</a></div>
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<div>Best,</div>
<div>Matej</div>
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<div style="font-family: Consolas; font-size: medium;">Dr. Matej Repic</div>
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<div><font face="Consolas">Ecole Polytechnique Fédérale de Lausanne</font></div>
<div><font face="Consolas">Laboratory of Computational Chemistry and Biochemistry</font></div>
<div><font face="Consolas">SB - ISIC – LCBC</font></div>
<div><span style="font-family: Consolas;">BCH 4108</span></div>
<div><font face="Consolas">CH - 1015 Lausanne</font></div>
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<span style="font-weight:bold">From: </span><<a href="mailto:chimera-users-bounces@cgl.ucsf.edu">chimera-users-bounces@cgl.ucsf.edu</a>> on behalf of "Flaherty, Daniel P" <<a href="mailto:dflaher@purdue.edu">dflaher@purdue.edu</a>><br>
<span style="font-weight:bold">Date: </span>Friday, August 7, 2015 at 04:38<br>
<span style="font-weight:bold">To: </span>"<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>" <<a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>
<span style="font-weight:bold">Subject: </span>[Chimera-users] Help Generating Spheres<br>
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<div>Hello,</div>
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<div>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 (<a href="http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm">http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm</a>).</div>
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<div style="font-family: Calibri;"><font face="Calibri,sans-serif">In the section where it says,"</font><span style="font-family: Arial, Helvetica, sans-serif; font-size: 18px;">To generate the spheres, simply use the command "</span><span class="SpellE" style="font-family: Arial, Helvetica, sans-serif; font-size: 18px;">sphgen</span><span style="font-family: Arial, Helvetica, sans-serif; font-size: 18px;">"
in the same folder that contains the INSPH and the rec.ms files. The output will be two files: </span><a href="http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/rec.sph" style="color: rgb(0, 0, 0); font-family: Arial, Helvetica, sans-serif; font-size: 18px;"><span class="SpellE">rec.sph</span></a><span style="font-family: Arial, Helvetica, sans-serif; font-size: 18px;">,
which contains the spheres in clusters, and </span><a href="http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/OUTSPH" style="color: rgb(0, 0, 0); font-family: Arial, Helvetica, sans-serif; font-size: 18px;">OUTSPH</a><font face="Arial,Helvetica,sans-serif"><span style="font-size: 18px;">,
which contains general information about the calculation.” </span></font></div>
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<div style="font-family: Calibri;">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."</div>
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<div style="font-family: Calibri;">Any help would be greatly appreciated!</div>
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<div style="font-family: Calibri;">Thanks,</div>
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<div style="font-family: Calibri;">Dan</div>
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