Re: [ccp4bb] refining anisotropy B factors on only a subset of atoms

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

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Subject: Re: refining anisotropy B factors on only a subset of atoms
From: Ethan Merritt merritt {- at -} U {- dot -} WASHINGTON {- dot -} EDU
Date: 2008-12-11

On Tuesday 09 December 2008 11:22:04 Joseph Ho wrote:
> Hello,
>
> I have a refined 1.8A structure that I wonder if I could squeeze out some anisotropy information. I did TLS refinement on the protein, and it helped my Rfree. But I would like to ask a biological question based on the thermal movement of only a few waters (7 total). In theory, that is not adding a lot of parameters for anisotropy refinement because I am not refining anisotropy of the whole protein. Correct me if I am wrong. So,
>
> 1) How do I use Refmac to refine anisotropic B's on only 7 waters?
> There is an option to use "mixed" for B factor refinement, but I don't know how to define the atoms.

You can just add ANISOU records for a selected set of atoms.
Start with an isotropic description (off-diagonal terms = 0; diagonal terms equal to each other).
But...

> 2) If this can be done, given my resolution, how much confidence can I put in my anisotropy
> refinement of those waters? In another word, if I do see thermal ellipsoids of the waters,
> are they believable? And if I don't, is it because my resolution isn't high enough to see it anyways?

I would definitely not believe anisotropic refinement of individual waters
at 1.8A resolution.

Some while ago I ran tests by starting with a <1.0 A fully-aniso structure and
gradually truncating the resolution of the data used for refinement. That way I
could compare the resulting Uij values back against those obtained at high
resolution. With sufficiently strong restraints, I could make the protein atoms
more or less behave down to about 1.6A resolution, although the result was
less good than using TLS refinement instead. However, by that point
the Uij values for water atoms were not even mathematically stable, let alone
reliably correlating with the "true" values.

> I have a total of ~1700 atoms, and ~24000 unique reflections at 1.8A resolution.
>
> Thanks!
> Joseph

--
Ethan A Merritt
Biomolecular Structure Center
University of Washington, Seattle 98195-7742

CCP4bb navigation

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

Previous message:
Subject: Postdoctoral Research Positions
From: "L {- dot -} Wayne Schultz" schultz {- at -} HWI {- dot -} BUFFALO {- dot -} EDU
Date: 2008-12-11

Next message:
Subject: Re: MR with DNA
From: Phoebe Rice price {- at -} UCHICAGO {- dot -} EDU
Date: 2008-12-11