Re: [phenixbb] Refinement Problem

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: [email protected] [[email protected]] on behalf of Kay Diederichs [[email protected]] Sent: Thursday, January 13, 2011 5:08 PM To: [email protected] Subject: Re: [phenixbb] Refinement Problem

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Date: Wed, 12 Jan 2011 17:12:04 -0500 (EST) From: Christopher W Davies To: [email protected] 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-fac...

HTH,

Kay _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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