[phenixbb] How do I turn off sidechain rotamer fitting?
owen at scripps.edu
Mon Jul 15 12:51:20 PDT 2013
I'm now doing paired refinement with and without real space refinement
and will send you the files when they are done.
On Jul 15, 2013, at 3:03 PM, Pavel Afonine wrote:
> 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
> 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,
>> 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.
>> 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
>>> explain this to me off list and send files so I can reproduce the
>>> On 7/15/13 10:46 AM, Owen Pornillos wrote:
>>>> I'm using one of the nightlies - dev 1427. It's not doing very
>>>> in combination with NCS. Or what is the most recent nightly that
>>>> not have this feature?
>>>> Many thanks,
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
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