<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><DIV>On Jun 9, 2007, at 7:52 AM, figo wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> I have seen your solution to the dock prep in batch mode (<A href="http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-May/001043.html">http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-May/001043.html </A>) , but when I run the command : chimera --nogui pdb:1gcn dockprep.py , the chimera want to Fetch protein 1gcn from web site <A href="http://www.rcsb.org">www.rcsb.org</A>, I have download the entire PDB, so how can I specify the PDB path to the chimera? Thanks. </BLOCKQUOTE><BR></DIV><DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>If you have the PDB files laid out the same way that the RCSB distributes them (e.g. entry 1GCN is in gc/pdb1gcn.ent) then Chimera will automatically look in /mol/pdb and /usr/mol/pdb for them. To have it look elsewhere you need to edit the file <your Chimera installation>/share/chimera/pdbDir and follow the reasonably simple instructions contained in that file. The drawback is that you will need to do that edit every time you install a new Chimera. Putting a better mechanism in place is on our to-do list.</DIV><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>Other alternatives include putting the full path to the PDB file in your command, or putting all the files you need into one directory and using the PDB preferences (Favorites...Preferences...[change to PDB category]) to get Chimera to look in that directory.<BR><DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> Eric Pettersen</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> UCSF Computer Graphics Lab</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> <A href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> <A href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</A></DIV></DIV></DIV><DIV><BR class="khtml-block-placeholder"></DIV></BODY></HTML>