[phenixbb] NCS in mr_rosetta

Thu May 15 08:03:42 PDT 2014

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-contents.html

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: 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)
> -------------------------------------------------------------------------------------------------------
>
>
>
> 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
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>> ------
>> 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
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb