[phenixbb] Refinement of perfect twined data of P31/P32

Pavel Afonine pafonine at lbl.gov
Mon Apr 22 08:26:19 PDT 2013


just to second Nat's reply - yes, if you send the files to 
help at phenix-online.org I will be happy to have a look.

I've seen cases which are genuinely troublesome (and which we may not be 
able to help much with given how much time we can afford to spend), but 
also I witnessed situations where an "R-factor and refinement" trouble 
like this was due to using Iobs calling them Fobs (or something like 
this obviously wrong and simple to detect and correct).


On 4/22/13 7:57 AM, Nathaniel Echols wrote:
> On Mon, Apr 22, 2013 at 7:45 AM, miyatake <miyatake at riken.jp> wrote:
>> Now I'm triying to refine almost perfect twining data
>> (mixing of P31 and P32). It has a twining operation of (h, k, l) = (-h, -k, l),
>> detected by the xtriage program.
>> The data qualigy seems to be good, deflacting to 1.6A resolution with Rmerge ~ 5%.
>> When I refined the MR structures with phenix.refine, however, the model geometries have been worse as over the 20% residues fall into disallowed Ramachandran region,
>> and Rfree stacked around 30%.
>> I tried many options such as real space refinement, SA, bad rotamer fixation, NCS restrain,,.., but they seem to be not so effective as usual twininig cases..
>> One molecule consists of 202 residues, and three molecules are inolved in AU.
>> Of course, I used the twin option (-h, -k, l) during the refinement.
>> Manual collection of the models could not improve the model anymore.
>> Would anyone please advise me how should I refine the twinned data?
> This sounds pathological (and/or a bug), but it's difficult to tell
> without looking at the model and data - would you be willing to send
> the files to us privately?  (I'm sure Pavel will want to see it too,
> so help at phenix-online.org is the best address for this.)
> One suggestion would be to run AutoBuild - with 1.6Å data it should
> work very well (as long as you enter the appropriate twin law).
> thanks,
> Nat
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