<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">As per Elaine's mail, great cover! As for the session issue, since the last production release I've completely redone session handling. There are no longer PDB files embedded in sessions. Instead, structures are built directly by the session. Also, attributes that are the same for all atoms (or residues/molecules) are recorded once instead of once per atom. As a result, sessions are smaller, use less memory when restoring, and restore faster. This new session code is in the 1.2224 snapshot release. If you try out 1.2224 and you still can't get a newly-saved session to restore (i.e. a session that was written using 1.2224), then let me know and I'll investigate to see if there are further bottlenecks I can eliminate.<DIV><BR class="khtml-block-placeholder"></DIV><DIV>--Eric</DIV><DIV><BR><DIV> <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>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>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="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></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"> </DIV><BR><DIV><DIV>On May 22, 2006, at 4:17 PM, Jonathan Hilmer wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Notepad++ will do a great job of editing the .py files.<SPAN class="Apple-converted-space"> </SPAN>I've found</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">that this is an extremely convenient way to accomplish certain tasks,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">such as precise alignment of multiple clipping planes.<SPAN class="Apple-converted-space"> </SPAN>However, you</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">definitely have to know what you're looking for when digging through</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the files.</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; ">On a related issue, I have a question regarding the saved sessions.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">In some of the viral capsid models I've created a saved session is</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">enormous (about 60 megabytes) and fails to compile either</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">automatically when loading the .py session or manually using the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">python.exe included with Chimera.<SPAN class="Apple-converted-space"> </SPAN>It seems to be a result of</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">excessive explicit attribute assignments that I don't really care</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">about (color etc) since they are easy enough to set once the model has</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">loaded.</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; ">Does anyone have any suggestions or experience with this issue?</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; ">Jonathan</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; ">PS: Check out the most recent issue of Science.<SPAN class="Apple-converted-space"> </SPAN>Although the editors</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">chose the least visually impressive submission, non of the variations</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">would have been possible without Chimera: great program.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hello. My name is Anne Szklarski and I am a student at The College of New</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Jersey. I was wondering if there was a way that the python files could be</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">modified in notepad. Does it require the Python software? The reason I ask</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">is because I have been renaming certain atoms in the .ent files using</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">notepad so that I may specifically select them in chimera. The only</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">problem with my current method is that I have to start the rendering</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">process from the beginning which is quite time consuming. So I was</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">wondering if there was a way that I could alter the chimera file directly</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and not lose any of the colors, etc. that I have chosen. I appreciate any</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">information on this matter.</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; ">Thank you,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Anne Szklarski</DIV> </BLOCKQUOTE><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; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@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/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>