[phenixbb] NCS in mr_rosetta

[Stefan Knight]

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

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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 17:49, 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)
>>> -------------------------------------------------------------------------------------------------------
>>> 
>>> 
>>> 
>>> _______________________________________________
>>> 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
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> Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk
>