Dear Eric,

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!

Have  a nice day,
Vincent


On 11/16/2011 08:31 PM, Eric Pettersen wrote:
Hi David,
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.
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.
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.
Anyway, let me know how you want your extension to work and I can provide the proper know-how for you to get going.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Nov 16, 2011, at 12:52 AM, david gfeller wrote:

Dear Chimera developer,

I've been working recently on a database on non-natural sidechains (http://www.swisssidechain.ch). Among else, we've developed a novel approach to accurately predict rotamers and our paper will be submitted within a few days.

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.

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.