Re: [phenixbb] NCS in mr_rosetta

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: [email protected] ------------------------------------------------------------------------------------------------------- "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) ------------------------------------------------------------------------------------------------------- On 14 May 2014, at 17:49, Randy Read 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 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: [email protected]

------------------------------------------------------------------------------------------------------- "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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------ 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk