[phenixbb] NCS in mr_rosetta
Stefan Knight
stefan.knight at icm.uu.se
Thu May 15 01:32:29 PDT 2014
Hi Tom,
The MR step did find 3 copies (or more like 2 ½ after remodelling/rebuilding) but the copies (together with their sg symmetry related copies) do not have 3 fold symmetry. I think this case is a very difficult one given that sequence identity is only 26%, 6 copies per asymmetric unit would correspond to
50% solvent (so there could be even more copies), and the structure is a jelly roll like beta barrel. I’m thinking that incorporating the prior knowledge of a 3-fold perpendicular to the monoclinic 2-fold might significantly increase the chance of success at the MR stage.
Best,
Stefan
-------------------------------------------------------------------------------------------------------
Stefan D. Knight, PhD
Professor of Biology
Department of Cell and Molecular Biology, Uppsala University
Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala
Sweden
Voice: +46 (0)18 471 45 54
Fax: +46 (0)18 53 03 96
E-mail: stefan at xray.bmc.uu.se
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"We trained very hard, but it seemed that every time we were beginning to
form into teams, we would be reorganised. I was to learn later in life that
we tend to meet any new situation by reorganising - and a wonderful method
it can be for creating the illusion of progress while producing confusion,
inefficiency and demoralisation."
– Gaius Petronius Arbiter (d. AD 66)
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On 14 May 2014, at 17:10, Terwilliger, Thomas C <terwilliger at lanl.gov> wrote:
> Hi Stefan,
>
> Normally mr_rosetta figures out the NCS from the MR solution itself, as opposed to using anything in the data. It would seem that the MR step should have found 3 copies and then mr_rosetta should have noticed that. I wonder if somehow the MR step didn't find multiple copies?
>
> All the best,
> Tom T
>
> On May 14, 2014, at 7:13 AM, Stefan Knight wrote:
>
>> Hi,
>>
>> Is there some way to make mr_rosetta use information about NCS present in the data? I have data from a crystal in sg P21 with a clear 3-fold axis perpendicular to the two-fold screw (as seen in self rotation function), and most likely 6 molecules in the asymmetric unit, but none of the mr_rosetta solutions that have appeared so far show 3-fold symmetry, and it doesn’t seem like the ncs is used in the search. The only info about ncs in mr_rosetta I have been able to find online pertains to extracting NCS from search models or mr_rosetta assembled models.
>>
>> Thanks,
>> Stefan
>>
>> -------------------------------------------------------------------------------------------------------
>> Stefan D. Knight, PhD
>> Professor of Biology
>> Department of Cell and Molecular Biology, Uppsala University
>> Uppsala Biomedical Centre, P.O. Box 596, S-751 24 Uppsala
>> Sweden
>>
>> Voice: +46 (0)18 471 45 54
>> Fax: +46 (0)18 53 03 96
>> E-mail: stefan at xray.bmc.uu.se
>>
>> -------------------------------------------------------------------------------------------------------
>> "We trained very hard, but it seemed that every time we were beginning to
>> form into teams, we would be reorganised. I was to learn later in life that
>> we tend to meet any new situation by reorganising - and a wonderful method
>> it can be for creating the illusion of progress while producing confusion,
>> inefficiency and demoralisation."
>>
>> – Gaius Petronius Arbiter (d. AD 66)
>> -------------------------------------------------------------------------------------------------------
>>
>>
>>
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