<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>From: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">Alex Gawronski <<a href="mailto:alex.gawronski@gmail.com">alex.gawronski@gmail.com</a>></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Date: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica">August 4, 2009 1:28:42 PM PDT</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>To: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><b>Subject: </b></font><font face="Helvetica" size="3" style="font: 12.0px Helvetica"><b>Re: [Chimera-users] Minimize</b></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div> </div>Hello again,<br><br>Is there a way to run Dock Prep, without GUI, from a script or command line? I tried 'start Dock Prep' with the headless linux version and it gave me a "<span dir="ltr"></span>ImportError: No module named Togl". <br> <br>Thanks,<br>Alex</blockquote></div></div></blockquote><br></div><div>You have to use a Python script in Chimera. Something along the lines of:</div><div><br></div><div>from chimera import openModels, Molecule, runCommand</div><div>from DockPrep import prep</div><div>prep(openModels.list(modelTypes=[Molecule]))</div><div>runCommand("write out.pdb")</div><div><br></div><div>which you would then use in Chimera in a fashion similar to this:</div><div><br></div><div>chimera --nogui structure001.pdb script.py</div><div>mv out.pdb processed/structure001.pdb</div><div><br></div><div><br></div><div>There are keyword arguments to the prep() function for changing it's behavior in the same fashion as the check buttons do in the DockPrep graphical interface.</div><div><br></div><div>If you're familiar with Python you could modify the script to loop through your files directly in one instance of Chimera rather than calling Chimera once for each file.</div><div><br></div><div>--Eric</div><div><br></div><br></body></html>