<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">You're welcome! Thanks for making the suggestion -- a lot of people are making use of it.<div><br></div><div>--Eric</div><div><br><div><div>On Nov 16, 2011, at 11:50 PM, Vincent Zoete wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"> <meta content="text/html; charset=ISO-8859-1" http-equiv="Content-Type"> <div bgcolor="#ffffff" text="#000000"> Dear Eric,<br> <br> By the way, thank you very much for having added the possibility to invert the configuration of chiral atoms in Chimera in response to our suggestion (#9474: RFE: chirality inversion). That will also be very useful!<br> <br> Have a nice day,<br> Vincent<br> <br> <br> On 11/16/2011 08:31 PM, Eric Pettersen wrote: <blockquote cite="mid:4639461D-7E87-494A-AF4D-1DB6386AB883@cgl.ucsf.edu" type="cite">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: 0px; font-size: 16px;"><font style="font: 16px Helvetica;" face="Helvetica" size="5"> Eric Pettersen</font></div> <div style="margin: 0px; font-size: 16px;"><font style="font: 16px Helvetica;" face="Helvetica" size="5"> UCSF Computer Graphics Lab</font></div> <div style="margin: 0px; font-size: 16px;"><font style="font: 16px Helvetica;" face="Helvetica" size="5"> <a moz-do-not-send="true" href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></div> <div><font style="font: 16px Helvetica;" face="Helvetica" size="5"><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 moz-do-not-send="true" 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> <br> <fieldset class="mimeAttachmentHeader"></fieldset> <br> <br> <fieldset class="mimeAttachmentHeader"></fieldset> <br> <br> <br> <div apple-content-edited="true"> </div> <br> </blockquote> <br> </div> _______________________________________________<br>Chimera-dev mailing list<br><a href="mailto:Chimera-dev@cgl.ucsf.edu">Chimera-dev@cgl.ucsf.edu</a><br>http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev<br></blockquote></div><br></div></body></html>