<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Perhaps the situation is that you have the same session using dozens or hundreds of copies of the same PDB file?<div><br></div><div>--Eric</div><div><br><div><div>On Jun 23, 2010, at 1:47 PM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Jun 23, 2010, at 12:48 PM, Dougherty, Matthew T wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi,<br><br>When PDF files are read by Chimera and the session is written, the PDB data becomes part and parcel with the session files. That is, Chimera does not go back to the PDB files when it reloads the session, it uses the PDB data within the session file instead; as contrasted to density volume files, which are referenced by the session file, and the density volume files reloaded when the session file is read by Chimera.<br><br>Is there a way to force the session file not to save the PDB internally to the session file, and instead reference and interact with it similar to the way volume files are managed?</div></blockquote><br></div><div>Hi Matthew,</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Briefly: no. For a variety of reasons:</div><div><br></div><div>1) Structural data didn't necessarily come from PDB files.</div><div>2) What to do about structure deletions and additions?</div><div>3) Session is less transportable/publishable (also occurs with volume files separate from sessions) </div><div><br></div><div>I don't see any upside really. You wouldn't be able to swap in a different PDB file because there would structure attributes stored in the session file (charges, conservation scores, etc.) that would need to be mapped on a 1-for-1 basis with atoms/residues of the original PDB file. I guess if your PDB file was huge there would be some space savings from having multiple sessions referencing the same PDB file. Nonetheless, the space issue is a lot less important for structure files than volume files.</div><div><br></div><div>--Eric</div><br><div apple-content-edited="true"> <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; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-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: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>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: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>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: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div><br class="Apple-interchange-newline"></div></span> </div><br></div>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></blockquote></div><br></div></body></html>