[Chimera-users] add custom residues to rotamer library or for swapaa command

Eric Pettersen pett at cgl.ucsf.edu
Mon Dec 5 10:58:10 PST 2011

If SwissSideChain doesn't cover your needs I can send you the same  
info I sent the SwissSideChain people so they could get their plugin  
working.  Your rotamers would need to be in Dunbrack format, and then  
you would still have to do some work but not too much.


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Dec 5, 2011, at 10:49 AM, Elaine Meng wrote:

> Hi Sabuj,
> There is no user interface way to do that (you'd have to get into  
> code)... however, your question is quite timely, as there is a new  
> plugin that provides a Rotamers-type interface to hundreds of  
> nonstandard residues.  It also makes a new command "swapnaa" to  
> access these residues via command line.
> This SwissSidechain plugin is provided by the Molecular Modelling  
> Group at SIB.  Information and download:
> <http://ludwig-sun1.unil.ch/~dgfeller/SwissSidechain/chimera.html>
> You can browse the SwissSidechain database to see if it includes  
> your residue of interest:
> <http://ludwig-sun1.unil.ch/~dgfeller/SwissSidechain/table.html>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Dec 5, 2011, at 10:31 AM, Sabuj Pattanayek wrote:
>> Hi,
>> How do I add custom residues so that they're usable with swapaa or  
>> the
>> rotamer tool?
>> Thanks,
>> Sabuj
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> Chimera-users at cgl.ucsf.edu
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