[phenixbb] Highly anisotropic data
rjr27 at cam.ac.uk
Wed Oct 5 12:53:10 PDT 2016
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.
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.
> 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,
>> 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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