[chimera-dev] non-natural sidechains

[Eric Pettersen]

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.





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