<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Hi Sheng-You,</div><div><br></div><div>On Apr 10, 2013, at 8:58 AM, Huang, Shengyou wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div fpstyle="1" ocsi="0"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; "><div style="margin-top: 0px; margin-bottom: 0px; "><font color="#000000" size="3" face="Arial">Dear Chimera developers,</font></div><div style="font-family: 'Times New Roman'; color: rgb(0, 0, 0); font-size: 16px; "><div><div style="font-family: Tahoma; direction: ltr; color: rgb(0, 0, 0); font-size: 10pt; "><p style="margin-top: 0px; margin-bottom: 0px; "><font size="3" face="Arial"></font> </p><div style="margin-top: 0px; margin-bottom: 0px; "><font size="3"><font color="#000000" face="Arial">Thank you for developing such a great and convenient software<a></a><span class="Apple-converted-space"> </span>package.</font></font></div></div></div></div></div></div></span></blockquote><div><br></div>Thanks! I'm glad you find it useful.</div><div><br><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div fpstyle="1" ocsi="0"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; "><div style="font-family: 'Times New Roman'; color: rgb(0, 0, 0); font-size: 16px; "><div><div style="font-family: Tahoma; direction: ltr; color: rgb(0, 0, 0); font-size: 10pt; "><div style="margin-top: 0px; margin-bottom: 0px; "><font size="3"><font color="#000000" face="Arial">Is there a way to use commands to select/identify those incomplete sidechains<a></a><a></a><span class="Apple-converted-space"> </span>of a protein?</font></font></div></div></div></div></div></div></span></blockquote><div><br></div>No, not without some monkeying around with Python. But the monkeying around is fairly simple in this case. Just take the Python code I've attached below and save it in a file that ends with ".py". Then you can use the "open" command to open the file, which executes the code. It will print the residues that are incomplete to the reply log. The code is basically a straight copy of the same code from Dock Prep, with a few mods to make it work as an independent script.</div><div><div><br></div><blockquote type="cite"><div fpstyle="1" ocsi="0"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; "><div style="font-family: 'Times New Roman'; color: rgb(0, 0, 0); font-size: 16px; "><div><div style="font-family: Tahoma; direction: ltr; color: rgb(0, 0, 0); font-size: 10pt; "><div style="margin-top: 0px; margin-bottom: 0px; "><font size="3"><font color="#000000" face="Arial">In addition, is it possible to do the DockPrep<a></a><span class="Apple-converted-space"> </span>job using commands instead of menu?</font></font></div></div></div></div></div></div></blockquote><div><br></div>Again, not directly. Is the purpose of this to execute Dock Prep in batch mode? If so, this message from the dock-fans mailing list describes how to do that:</div><div><br></div><div><a href="http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html">http://mailman.docking.org/pipermail/dock-fans/2007-May/001043.html</a></div><div><br><blockquote type="cite"><div fpstyle="1" ocsi="0"><div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0, 0); font-size: 10pt; "><div style="font-family: 'Times New Roman'; color: rgb(0, 0, 0); font-size: 16px; "><div><div style="font-family: Tahoma; direction: ltr; color: rgb(0, 0, 0); font-size: 10pt; "><div style="margin-top: 0px; margin-bottom: 0px; "><font size="3"><font color="#000000" face="Arial">Thank you very much for your help!</font></font></div></div></div></div></div></div></blockquote><div><br></div>You're welcome!</div><div><br></div><div>--Eric</div><div><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> UCSF Computer Graphics Lab</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> <a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></span></div><div><br></div><div></div></body></html>