kellerj at janelia.hhmi.org
Tue Mar 31 14:33:44 PDT 2015
By the way, if you don't already know, Phenix does not support multiple twin operators. Refmac in CCP4 does, and everything is automatic.
From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Tim Gruene
Sent: Tuesday, March 31, 2015 4:49 PM
To: phenixbb at phenix-online.org
Subject: Re: [phenixbb] twinning
as you provide a twin law you basically half the data to parameter ratio, your R-factor usually drops irrespective of whether your model improved or not. You need to judge by yourself, e.g. by the quality of the map, whether or not the twin operator actually caused an improvement of your model.
On 03/31/2015 06:47 PM, Shun Liu wrote:
> Dear Randy,
> Thank you so much for your suggestion. Phenix.xtriage indicated that there are 3 possible twin operators, (-h, -k, l; h, -h-k, -l; -k, -h, -l). When I provided twin law=-h,-k,l to phenix.refine (as it seemed that only one operator can be provided), I got lower R-factors than before. Now the question is that: should I provide all the three twin operators at the same time? And how? Thanks!
> On Mar 31, 2015, at 3:26 AM, Randy Read <rjr27 at cam.ac.uk> wrote:
>> Dear Shun,
>> Phaser does a test based on the moments of the intensity distribution, after correcting for anisotropy and (if present) translational non-crystallographic symmetry. However, once a test like that has indicated that twinning is probably present, you will get a better result from running a program like phenix.xtriage, which will compare reflections related by possible twin operators and give a more precise idea of the twin fraction.
>> Since you've managed to get reasonable R-factors (even if they are higher than expected for 1.7A), the twin fraction is probably not too high. The best thing to do now is probably to run phenix.xtriage to get a suggestion for what the twin operator is, then you can provide that twin operator to phenix.refine, which will then: a) refine the twin fraction to give a much more precise estimate; b) correct for twinning in the refinement. Detwinning is not recommended any more, because it is better to refine against the original data.
>> 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 31 Mar 2015, at 06:18, Shun Liu <sliu.xtal at gmail.com> wrote:
>>> Dear all,
>>> Recently I have got a data set that diffracts to 1.7 angstrom. Images look good. During data processing I did not find anything that looks strange. However, when I was doing Phaser-MR, I got a warning: " Intensity moments suggest significant twinning (>5%). Tests based on possible twin laws will be more definitive." What does this mean? A twinning data set? I still found a solution and refined the model step by step, using the data (20-1.7 angstrom). It seems that the final model and map are acceptable. But R-factors are 0.24/0.28, very high. Does the twin cause the high R-factors? Is there a solution to detwin? Or are the R-factors acceptable for a twinning data set? Any suggestions are appreciated and thanks in advance!
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Dr Tim Gruene
Institut fuer anorganische Chemie
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