<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Mar 31, 2009, at 3:03 PM, Matthew Dougherty wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Normally when Chimera saves a session it includes the PDB data as part <br>of the session file.<br><br>Is there a way to prevent that and have the individual pdb models <br>saved as PDB files?</div></blockquote><div><br></div>The short answer is no.<br><br></div><div>Chimera originally preserved molecular data as embedded PDB files in it's session files (embedded as strings). Over time it became clear that this was problematic because a) PDBs are pretty verbose and slow to parse, and b) some molecular data is just problematic to store in PDB format. In particular, the 5-digit limit for atom serial numbers in CONECT records is a deal breaker. So two and a half years ago (1.2304 release) the embedded-PDB-file approach was abandoned and the data was simply stored as Python lists and dictionaries. This resulted in smaller session files with faster restore times and less memory use. We anticipate using Python's pickle mechanism to further reduce restore times and memory use (during the .pyc compile) in the next release. So the only part of the PDB file preserved more or less intact is the header lines (as a dictionary of lists of strings). So the long answer is also no!</div><div><br></div><div>Sorry.</div><div><br></div><div>--Eric</div><div><div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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; "><br class="Apple-interchange-newline"> 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></div></div><br><div></div></div></body></html>