[phenixbb] NCS in mr_rosetta
Stefan Knight
stefan.knight at icm.uu.se
Thu May 15 01:32:26 PDT 2014
Hi Randy,
I think in really difficult cases (such as the one at hand) this could mean the difference between success and failure. I imagine it would at least in principle be relatively straightforward to incorporate NCS into the RF search, but I might well be missing something.
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
-------------------------------------------------------------------------------------------------------
"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 17:49, Randy Read <rjr27 at cam.ac.uk> wrote:
> The MR step in mr_rosetta is carried out by Phaser, which doesn’t have any way to exploit prior knowledge of NCS. It’s one of many things on a very long wish-list of features, but at the moment it’s not near the top of that list. If we hear of enough people who are constrained by the lack of such a feature, that of course will influence the order of the list!
>
> Best wishes,
>
> Randy Read
>
> On 14 May 2014, at 16:10, 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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>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
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>
> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research Tel: + 44 1223 336500
> Wellcome Trust/MRC Building Fax: + 44 1223 336827
> Hills Road E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
>
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