[phenixbb] Refinement Problem

Pavel Afonine pafonine at lbl.gov
Wed Jan 12 16:34:50 PST 2011


  If this is the case, then just:

- run AutoBuild (at 2.36A it should build your model no problems) or
- try phenix.refine from the very latest PHENIX nightly build which does 
Dual Space Refinement (real/reciprocal)
- check for twinning and if present then use it, etc...

http://www.phenix-online.org/download/nightly_builds.cgi

Pavel.


On 1/12/11 2:45 PM, Christopher W Davies wrote:
> I am fairly certain that I have the correct space group.  I had initially processed my data in P3, P31, and P32, however, I could not obtain a molecular replacement solution.  I then went back to APS and reprocessed my data in higher space groups and I found three more space groups, P321, P3121, and P3221.  P3221 was the only space group to give me a molecular replacement solution.
>
> Thanks for you help.
>
> Chris
>
> ----- Original Message -----
> From: "Kelly Daughtry"<kddaught at bu.edu>
> To: "PHENIX user mailing list"<phenixbb at phenix-online.org>
> Sent: Wednesday, January 12, 2011 5:15:40 PM
> Subject: Re: [phenixbb] Refinement Problem
>
>
>
> Hello Chris, The standard question here is: Are you certain of your space group? That seems to be the main culprit behind R factors that wont decrease.
> Can you provide some statistics showing your confidence in your space group?
>
>
>
> Kelly Daughtry
>
> *******************************************************
> Kelly Daughtry, Ph.D.
> Post-Doctoral Fellow, Raetz Lab
> Biochemistry Department
> Duke University
> Alex H. Sands, Jr. Building
> 303 Research Drive
> RM 250
> Durham, NC 27710
> P: 919-684-5178
> *******************************************************
>
>
>
> On Wed, Jan 12, 2011 at 5:12 PM, Christopher W Davies<  cdavies at purdue.edu>  wrote:
>
>
>
>
> I am having an issue with refining my structure. I have a 2.36 A resolution dataset. I have found a solution by molecular replacement in the space group P3221. I have been refining the structure, however, my Rfactor/Rfree are not decreasing even though I have good density. My current Rfactor/Rfree values are .40/.43. Can anyone help me?
>
>
> Thanks.
>
> Chris
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