[chimera-dev] non-natural sidechains

[Eric Pettersen]

You're welcome!  Thanks for making the suggestion -- a lot of people  
are making use of it.

--Eric

On Nov 16, 2011, at 11:50 PM, Vincent Zoete wrote:

> 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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