<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi David,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I'd be happy to help you get your extension working. Do you envision your extension being a separate tool that provides its own interface, or instead being integrated into the Rotamers tool and simply being listed as another possible rotamer library? I'm guessing the latter since I don't think you'd care about the format of Chimera's rotamer libraries otherwise, but let me know so I know what kind of guidance to provide. If integrating with Rotamers, I will need to change some code [which I'm perfectly happy to do!] since Rotamers only handles standard amino acids right now.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>You should probably omit chimera-dev on any replies since we'll be getting into hairy minutiae that is unlikely to be of interest to others.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Speaking of hairy minutiae, the rotamer files aren't encrypted per se, but have been converted to a binary format that can be read a lot faster by Chimera. I have attached the Python scripts that were use to convert backbone-dependent files and backbone-independent files into the zip archives that Chimera uses. They should "just work" on your files since you use the Dunbrack format.</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Anyway, let me know how you want your extension to work and I can provide the proper know-how for you to get going.</div><div><br></div><div>--Eric</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "> Eric Pettersen</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font-size: 16px; "><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-size: 16px; "><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><font face="Helvetica" size="5" style="font: normal normal normal 16px/normal Helvetica; "><br></font></div><div><div>On Nov 16, 2011, at 12:52 AM, david gfeller wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear Chimera developer,<br><br>I've been working recently on a database on non-natural sidechains (<a href="http://www.swisssidechain.ch">http://www.swisssidechain.ch</a>). Among else, we've developed a novel approach to accurately predict rotamers and our paper will be submitted within a few days.<br> <br> I'd be very interested to develop a Chimera extension to visualize them (so far, we only have a PyMOL plug-in). I have rotamer library files in the same format as the Dunbrack 2002 rotamer library for each of the >200 sidechains included in my database. However, it appears that rotamer files (dependentRotamerData.zip) are encrypted in Chimera and I could not figure out how this encryption is done.<br> <br>I was wondering if you could advise me something to help me (especially whether there are some hard-coded part that would need to be modified to include new sidechains in Chimera) and if you'd be interested in such an extension.</blockquote><br></div><div><br></div></div></body></html>