Re: [ccp4bb]: Anisotropic B-factors

[Bart Hazes <bhazes@ualberta.ca>]

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On Thu, 4 Apr 2002, Konstantinos Beis wrote:

> Dear All,
> I am working with some data at very high resolution (1.5A). The protein has
> a substrate and a cofactor (NADH). I have refined the structure both
> isotropically and anisotropically (in the presence and absence of the
> cofactor). We are interested in the puckering of the NADH ring. I would
> like to plot the anisotropic B-factors of the cofactor as ellipsoids. So
> far, I have only tried Rastep in RASTER3D but I do not really understand
> the way that it draws the plot. Does anybody have any suggestions on how to
> do so?

1.5A is still marginal for anisotropic B-factor refinement. Check your Rfree
and adjust your anisotropy restraints as needed to make sure you are improving
your model and not just the Rfactor. You (c/sh)ould also test the TLS
refinement in Refmac5 for the protein, your cofactor or both.

For display you can use Xfit. In the "view" menu you can select "Thermal
Ellipse" "Thermal axes" or both to draw the anisotropic B-factor ellipsoids
and their main axes, respectively.

Bart

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