Dear Urmi,
The way you switched from Phenix to Refmac may not have resulted in the flat
B-factor model in Ethan's paper. You should really do a thorough test in which
you reset the B-factors before you start refinement. Shameless plug: PDB_REDO
will do this automatically and has a few fallback options for cases in which
the Hamilton test is inconclusive.
Your R-factors a quite low for your resolution which suggests that you may have
been a bit too conservative when picking your resolution cut-off. If you have
more data you can try using that as well. This may also help your choice of
B-factor model. It will improve your data/parameter ratio.
HTH,
Robbie
Netherlands Cancer Institute
www.cmbi.ru.nl/pdb_redo
Sent from my Windows Phone
________________________________
From: Ethan Merritt
Sent: 2013-01-25 01:36
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] B-factors
On Thursday, January 24, 2013 03:52:12 pm Urmi Dhagat wrote:
> Hi all,
>
> I have been refining twinned data (at 3.1 A resolution) using refmac. My R
> and Rfree values are 19.6 and 26.2 respectively with NCS restraints and
> isotropic B-factor refinement.. I am not sure weather it is a good idea to
> refine individual B-factors at this resolution.
>
> I have also tried refining the same model in phenix but this time not
> refining the Bfactors. My Rfactor and Rfree are 25 and 32 respectively.
> Refining with TLS in Phenix drops R factors to 23 and 29.
I would suspect it is possible to do better than that.
My thoughts on how to approach it were written up for a past CCP4 Study Weekend
and appeared in Acta D last year:
"To B or not to B" Acta D 68:468 (2012).
You can find a link to the PDF on the TLSMD web site
http://skuld.bmsc.washington.edu/~tlsmd/references.html
Ethan
> Then I used the output PDB from phenix and refined it in CCP4 (selecting
> overall B-factor refinement option instead of Isotropic) and my R factors are
> R work=16 and Rfree =21.
>
> If Rfree reflections are refined my refmac upon switching from phenix to
> refmac then does this contaminate the Rfree set ? Should swiching between
> refinement programs Phenix and Refmac be avoided?
>
>
> Urmi Dhagat
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
