[chimera-dev] non-natural sidechains

[Vincent Zoete]

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.
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