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Hi,<div><span class="Apple-tab-span" style="white-space:pre"> </span>The file "pdbDir" in the same directory as __init__.py defines what directory to look in for a PDB mirror distribution. If you change the contents of that file to:</div><div><br class="webkit-block-placeholder"></div><div>pdbDir = " /blah/blah/pdb/data/structures/divided/pdb"</div><div><br class="webkit-block-placeholder"></div><div>then Chimera will find your mirror distribution. The trouble is that if you install a new version of Chimera then that file will be overwritten. So I've just committed a change to Chimera so that if you have a file named "pdbDir" in ~/.chimera/chimera then that file will be used instead of the one inside the Chimera distribution. So if you get tomorrow's daily build it will have that change in it.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>The "system PDB mirror finding" needs to be improved somehow so that a system administrator can specify where the mirror is and not have to have individual users place files in their home directories to specify it.</div><div><br class="webkit-block-placeholder"></div><div>--Eric</div><div><br><div> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 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; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></span> </div><br><div><div>On Dec 17, 2007, at 5:12 AM, Moo Cow wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sorry for an easy question.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera has a hook to use a local mirror of the PDB (preferences-PDB)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I am too thick to see what path to give it. If you have the PDB,</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">you have the top level</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>/blah/blah/pdb</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the structure directory</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>/blah/blah/pdb/data/structures/all</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and the divided directory</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>/blah/blah/pdb/data/structures/divided/pdb</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">When a non-python reader looks at the code (__init__.py), it</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">seems to be trying out the divided directory</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>IDcode = IDcode.lower()</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>subpath = IDcode[1:3] + os.sep + "pdb" + IDcode + ".ent"</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>pdbDir = systemPDBdir()</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> <span class="Apple-tab-span" style="white-space:pre"> </span></span>if pdbDir is not None:</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>.....</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">but this does not look correct. The PDB divided path would want</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><span class="Apple-converted-space"> </span>subpath<span class="Apple-converted-space"> </span>IDcode[1:2]</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">to get the subdirectory "pt" from a file like "5pti"</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Many thanks and sorry for a seemingly daft question.</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><br></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--<span class="Apple-converted-space"> </span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Got No Time? 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