[phenixbb] Refinement Problem
epozh001 at umaryland.edu
Thu Jan 13 06:51:35 PST 2011
Aside from trying twinned refinement, consider reprocessing your
original data in a lower symmetry space group. Sometimes at relatively
low resolution, say, P21 has beta~90 and NCS closely resembling the
higher symmetry operators. Occasionally, data can be successfully
processed and molecular replacement "works" but R-values are stuck and
parts of the map are messy. First time I encountered this the map
looked well for the protein core but half of the loops were missing.
The most radical thing to do is to try P1 and if R-values do not drop
and density is not improved, then (unfortunately) you may have other
issues (e.g. twinning).
On Thu, 2011-01-13 at 11:47 +0000, Ms Chiung-Wen Chang wrote:
> i have similar issue as well
> i had ran the Xtrige and yep it was suspected as twinning dataset
> i can not define my space group so i ran bounch of space groups in the phaser
> i got solution for p22121
> every time i ran autobuild it failed ( my resolution is around 2.5)
> i have not tried the nightly-build yet -- but i will
> i open the map and model
> some part of model can fit nicely but some part are messy
> what sould i do ?
> im thinking to do map modification .... will it work ? i know the tool on ccp4 but i have not got it right ... always failed.....
> any suggestion ??
> From: phenixbb-bounces at phenix-online.org [phenixbb-bounces at phenix-online.org] on behalf of Kay Diederichs [kay.diederichs at uni-konstanz.de]
> Sent: Thursday, January 13, 2011 5:08 PM
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Refinement Problem
> > Date: Wed, 12 Jan 2011 17:12:04 -0500 (EST)
> > From: Christopher W Davies<cdavies at purdue.edu>
> > To: phenixbb at phenix-online.org
> > Subject: [phenixbb] Refinement Problem
> > 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
> there is a collection of things to think about at
> phenixbb mailing list
> phenixbb at phenix-online.org
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
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