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

Hi, I am surprised this hasn't been mentioned yet, but NCS has been used in MR searches for some time. Check out locked cross rotation and translation functions. The implementation of it I am familiar with is in GLRF and TF, from Liang Tong's lab (comes with amazing documentation by the authors, see references therein). Locked self/cross rotation functions may be valuable especially for those dealing with very high NCS, as in viruses. http://tonglab.biology.columbia.edu/Public/Replace/glrf/contents/glrf-conten... I also know that molrep and amore have implementations, but I am not too familiar with those. However, I have seen the locked RF/dyad searches being useful with molrep. Personally, I have been limited in cases where the number of NCS copies have been prohibitive to successful MR searches, so I would love to see NCS info incorporated into MR searches in Phaser, etc. In one case, where we had a 95%-identical MR model, all searches failed due to 12 copies in the asu. When the dimeric structure was solved and the problem was reduced to finding only 1/6th (~17%) of the diffracting mass in the asu at every search step, the MR search was readily successful (This was done at 3.9 A resolution using Phaser). I usually think when searching for less than 15% of the asu, one can fail regardless of search model quality. Another issue I had to contend with was improper (but not translational) NCS (that was the case in the 12-fold NCS), which may not be handled well by any algorithm/software. Anyway, I would vote for Phaser utilizing NCS information, if there were a vote on this. Engin On 5/15/14, 3:32 AM, Stefan Knight wrote:

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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---

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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

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