Re: [ccp4bb]: Anisotropic B-factors

[Ethan Merritt <merritt@u.washington.edu>]

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On Thursday 04 April 2002 01:20, Konstantinos Beis wrote:
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> 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?

Assuming that the residue you want is named NAD in the pdb file, you want
something like

	grep NAD file.pdb | rastep -auto -Bcol 5. 35. > ellipsoids.r3d
	render -jpeg < ellipsoids.r3d > ellipsoids.jpeg

That tells rastep to chose a nice view angle for your residue and
color the ellipsoids by B value.

If you want more control over the orientation you can compose the figure
interactively in Xfit and either create the Raster3D picture directly from
there or just save the orientation matrix for use in pictures you create from
the command line.

-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX:   (206)685-7002