Re: [ccp4bb]: A SAD case...

["David R. Cooper" <drc2n@unix.mail.virginia.edu>]

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Forgive me if this comes through twice.

On Wednesday 24 July 2002 10:30 am, OnLineHelpForm wrote:
>
> So, the question is: How is it possible this lack of density around the
> peaks if the figure of merit is 0.55, the phasing power 1.0-1.1 and the
> R-Cullis 0.85?  Have I got to discard the Se positions calculated by
> Shake-and-Bake?  Where could the error be? (As for the scripts I use to
> produce maps, they are pretty simple and had always worked, so it cannot  be
> just that.)

What version of SnB are you using?  I seem to recall that I had problems
with the output pdb files from SnB 2.1, even though the fractional
coordinate output was fine.  The SnB website  states the following about
version 2.2

"1.  The output coordinate file (name.SnB_pdb) is now orthogonalized
according to the PDB convention."

I haven't used SnB 2.2 yet, but this seems like it could be your problem.
Check it out by using coordconv (Convert Coordinate Utilities) to generate
a different version of the Se pdb file.

Good luck.
David

--------------------------------------------------------
David Cooper, Ph.D.
University of Virginia
Molecular Physiology and Biological Physics
PO BOX 800736
Charlottesville, VA 22908-0736