Re: [ccp4bb] Unusually low B factors after refinement

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Unusually low B factors after refinement
From: Kyle Dolan ktd {- at -} UCHICAGO {- dot -} EDU
Date: 2010-05-07

Next message:
Subject: increased RMS bondangle and RMS bondlength after twin refinement
From: Sudhir Kumar sudhir {- dot -} 1685 {- at -} GMAIL {- dot -} COM
Date: 2010-05-08

Subject: Re: Unusually low B factors after refinement
From: "Miller, Mitchell D {- dot -} " mmiller {- at -} SLAC {- dot -} STANFORD {- dot -} EDU
Date: 2010-05-07

Hi Kyle,
Are you refining with TLS? If so, then the default output will
be the residual B-factors. To get the full B-factors you need to
add the TLS component to the residual B's. This can be done
by re-running your refmac job with the keyword
TLSO ADDU

Note that this version of refmac will also add your waters to
TLS groups by default unless you give it the keyword
TLSD waters Exclude
So unless you included this keyword, then re-running refmac with
your same input file and the TLSO ADDU keyword is the
only way to ensure that your waters are converted to full B's as
the CCP4 program TLSANL cannot do this since the TLS definitions
in TLSOUT and the PDB header are not updated with regards to which
waters were assigned to different TLS groups. Also, if you
use the keyword TLSO ADDU, you should not use this PDB file
as input to your next round of refinement unless you also
use reset the B factors with the BFACtor SET ## keyword since
refmac expects residual B's on the input file.
I am not sure how many of these keywords are accessible via
the ccp4i interface or if you have to add them via the
run and view command file option if you use ccp4i.

Regards,
Mitch

-------------------------------
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kyle Dolan
Sent: Friday, May 07, 2010 3:12 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Unusually low B factors after refinement

Hello,

I am trying to run restrained refinement with Refmac5 (version 5.5.0109), including refinement of isotropic temperature factors, and I am seeing some very unusual behavior by the program. In the output pdb file, nearly all of the individual atomic B factors have a value of 2.0! My data is only to 2.9 Angstrom so I've been told to expect much larger atomic B factors. I am using anisotropy-corrected data (I ran my original data through the ellipsoidal truncation anisotropy correction server from UCLA), but when I repeated the run using the original uncorrected mtz file I still saw an average atomic B around 10. I also looked back at the output pdbs from some previous rigid-body refinements (using the same anisotropy-corrected data) and there the B factors are much higher, 50-100. I'm not sure how to prevent Refmac from making this mistake--can anyone offer a suggestion?

Thanks,
Kyle

Kyle T. Dolan
Department of Biochemistry and Molecular Biology
The University of Chicago
ktd@uchicago.edu

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Unusually low B factors after refinement
From: Kyle Dolan ktd {- at -} UCHICAGO {- dot -} EDU
Date: 2010-05-07

Next message:
Subject: increased RMS bondangle and RMS bondlength after twin refinement
From: Sudhir Kumar sudhir {- dot -} 1685 {- at -} GMAIL {- dot -} COM
Date: 2010-05-08