[phenixbb] Highly anisotropic data

Fri Oct 7 08:08:45 PDT 2016

Hi Kostya,

phenix.resolution

reports effective resolution of data set. It is based on methods 
described here:

J. Appl. Cryst. (2015). 48, 589-597
Acta Cryst. (2013). D69, 1921-1934

As I pointed out before, a single number for highest resolution isn't 
very informative unless you show data completeness per resolution (in 
phenix.refine log file it is reported in the beginning of macro-cycles 
right after bulk-solvent step).

Pavel

On 10/7/16 00:15, Kogan, Konstantin wrote:
> Dear all,
>
> Thank you for your comments. The maps are not that bad, and actually 
> from biological point of view we do see everything we want. One of the 
> questions is how to report the parameters for the structure, as I have 
> a feeling that the effective resolution is much lower than 2.64Å, 
> which is the current limit, and the mean B value is twice higher than 
> estimated Wilson B value. All together it seems that this is the data 
> I have, but I would like to be sure, that I have got maximum out of it.
>
> I attach the xtriage log file for more information, if needed. Also I 
> attached the example of a good map region at 1.6 sigma and a bad map 
> region at 1.0 sigma.
>
> I have also tested to refine at 2.8, 2.9, and 3.0, and I haven't seen 
> much difference in maps quality, but the Rwork/Rfree went down a bit.
>
> Isn't is seems a bit suspicious 2.64Å resolution, 
> Rwork/Rfree=0.28/0.31, and mean B value 114? Is there a way to 
> present/report effective resolution?
>
> Kostya
>
>
>
>
> Hi Kostya,
>
> how complete the data set is? Missing reflections in some resolution 
> zones between 2.64A and inf may be sufficient to make the effective 
> resolution lower or much lower than 2.64A which would explain why the 
> map does not look like what you expect.
>
> Pavel
>
>
> On 05/10/16 22:53, Randy Read wrote:
>> Hi,
>>
>> As Christian said, the level of anisotropy is not that bad for this 
>> structure.  In terms of what Phenix can do to handle it, first, when 
>> you solved it by MR, Phaser would have accounted explicitly for the 
>> anisotropy.  In fact, Phaser’s algorithms underlie the anisotropy 
>> server that produced your plot! Phenix.refine will also refine the 
>> overall anisotropy parameters.
>>
>> When you have really severe anisotropy, the current algorithms may 
>> not account well enough for the differing accuracy of reflections in 
>> the weak directions.  So it can sometimes be helpful to do 
>> anisotropic pruning of the data in the way that the anisotropy server 
>> implements it.  But this is something to do with some caution, and I 
>> think you should only press on with it if the maps allow you to see 
>> things you couldn’t see clearly before.
>>
>> Best wishes,
>>
>> Randy Read
>>
>> -----
>> 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
>>
>>> On 5 Oct 2016, at 20:32, Christian Roth <christianroth034 at gmail.com> 
>>> wrote:
>>>
>>> Hi Kostya,
>>>
>>> I have seen worse data than that, which are ususally treated quite 
>>> well within phenix using standard parameters. With a resolution of 
>>> about 2.7 Ang. I wouldn't expect to see waters and also just well 
>>> ordered side chains, whereas more flexible ones just give some 
>>> "bumps"  pointing away from the main chain density. Though without a 
>>> picture or something else it is difficult to say if your maps are 
>>> really unusually bad.
>>>
>>> Cheers
>>>
>>> Christian
>>>
>>> Am 05.10.2016 um 07:47 schrieb Kogan, Konstantin:
>>>> Dear all,
>>>>
>>>> I have highly anisotropic data. I was able to solve the structure 
>>>> by MR, and refine it with phenix.refine to Rwork/Rfree=0.28/0.31 
>>>> with Resolution cutoff 2.64Å and mean B values 114, which is pretty 
>>>> high for such resolution. Though the overall structure makes sense, 
>>>> the maps are quite featureless, no water molecules, and side-chains 
>>>> refinement is a problem. I have tested how the data is anisotropic 
>>>> with Diffraction Anisotropy Server (see attached image), which 
>>>> shows clearly, that we don't really have data to 2.64Å in all 
>>>> directions. Though, there are other servers/programs that can deal 
>>>> specifically with anisotropic data e.g. STARANISO anisotropy server 
>>>> and then refine with BUSTER, I would like to know if it's possible 
>>>> still to use Phenix with some more advance parameters to actually 
>>>> address the issue of anisotropy and to get maximum out of the data. 
>>>> The space group is P61 2 2, cell parameters are 73, 73, 453, 90, 
>>>> 90, 120 and I have high multiplicity data, but no NCS.
>>>>
>>>> Thanks in advance for any input,
>>>>
>>>> Kostya
>>>> -- 
>>>> Konstantin (Kostya) Kogan
>>>> Postdoctoral researcher
>>>> Pekka Lappalainen's Lab
>>>> Institute of Biotechnology
>>>> University of Helsinki
>>>> Helsinki, Finland
>>>> Mobile: +358-(0)45-8994342
>>>>
>>>>
>>>>
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