[ccp4bb] Stop Refmac from refining B factors?

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

Previous message:
Subject: Re: twin fraction varies between crystals?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-18

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Subject: Re: Stop Refmac from refining B factors?
From: "Harry M {- dot -} Greenblatt" harry {- dot -} greenblatt {- at -} WEIZMANN {- dot -} AC {- dot -} IL
Date: 2007-04-18

Subject: Stop Refmac from refining B factors?
From: Eva Kirchner eva {- dot -} kirchner {- at -} UNI-TUEBINGEN {- dot -} DE
Date: 2007-04-18

Hi,

I have a little problem with B-factor refinement. I'm using the CCP4i
interface, Refmac 5.2.0019, a resolution of 30-3.2 A (I tried 8-3.2 A as
well, it doesn't make a big difference for this problem), and a current
Rfree of 30.4%.

Refmac refines the B-factors so that they are nearly the same for main chain
and side chain, and I don't like that (or could it make sense in any way?).
Moreover, my structure is a protein complex, and Refmac is mainly doing this
for one component of the complex. If I take the B-factors from the original
uncomplexed protein (around 18, 1.75 A) and add 44 to them with moleman to
get them in the range they are in the complex, Refmac "flattens" them
remarkably in only 5 cycles of restricted refinement. Does anyone have an
explanation for this? I am pretty sure that the complex components are in
the right place, I see beautiful density and everything I should see at this
resolution.

Here is what I tried further:

* I de-selected "Refine isotropic temperature factors" in the Refmac
interface. There was no REFI BREF ISOT any more in the com file. But there
was also no difference in the B-factors compared to when there _was_ REFI
BREF ISOT in the com file... So does Refmac just _ignore_ my wish not to
refine B-factors? (The REFI keywords were as follows: type REST - resi MLKF
- meth CGMAT - is there any B-factor-thing hidden in this?)

* I played around with the geometric parameters. If I select the B-factor
values there (the keywords are TEMP
BFAC
), it does not make _any_ difference,
what values I fill in there, the resulting B-factors are always the same
(but different from when I don't use the TEMP keyword, and even "flatter").
Default for WBSCAL is 1.0, I tried 10, 1.0, 0.1, 0.01, and the equivalent
numbers for the sigbs.

Thanks for any thoughts on this,

Eva

CCP4bb navigation

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

Previous message:
Subject: Re: twin fraction varies between crystals?
From: Ian Tickle I {- dot -} Tickle {- at -} ASTEX-THERAPEUTICS {- dot -} COM
Date: 2007-04-18

Next message:
Subject: Re: Stop Refmac from refining B factors?
From: "Harry M {- dot -} Greenblatt" harry {- dot -} greenblatt {- at -} WEIZMANN {- dot -} AC {- dot -} IL
Date: 2007-04-18