[phenixbb] Refinement Problem

Ed Pozharski 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:
> hi 
> 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 ??
> thanks
> wenwen
> ________________________________________
> 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
> Chris,
> there is a collection of things to think about at
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Refinement#R-factor_does_not_go_down
> HTH,
> Kay
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Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------   / Lao Tse /

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