[phenixbb] How do I turn off sidechain rotamer fitting?

Pavel Afonine pafonine at lbl.gov
Mon Jul 15 12:03:43 PDT 2013

Hi Owen,

local real-space refinement will not fit a side-chain into a rotamer 
outlier: it uses both, map and rotamer library, and also it uses a quite 
complex logic that aims to find best density fit and at the same time 
keep good geometry (no outliers of any sort). That's why I wanted to 
look at the files because to me what you described is an indicator of a 
problem somewhere else or a bug..


On 7/15/13 11:56 AM, Owen Pornillos wrote:
> Hi Pavel -
> Thanks for the reply.
> I have a 2.6 A data set that has a dimer in the asymmetric unit, and 
> so I'm using NCS. Some of the big sidechain densities (LYS, ARG, etc.) 
> are not well-defined so I'd like to just restrain them to the other 
> chain. The auto rotamer fitting of course tries to fit them, and the 
> result is a list of half a dozen or so rotamer violations. I'm going 
> through the list to see if the density truly defines different 
> conformations. I think this is just a general run of the mill problem 
> with fitting/refinement with NCS.
> Thanks,
> Owen
> On Jul 15, 2013, at 1:55 PM, Pavel Afonine wrote:
>> Hi Owen,
>> you can disable it by turning of real-space refinement off.
>> I'm interested to know what exactly is not going well: could you please
>> explain this to me off list and send files so I can reproduce the 
>> problem?
>> Pavel
>> On 7/15/13 10:46 AM, Owen Pornillos wrote:
>>> I'm using one of the nightlies - dev 1427.  It's not doing very well
>>> in combination with NCS.  Or what is the most recent nightly that does
>>> not have this feature?
>>> Many thanks,
>>> Owen
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