Or Phenix.
Miles
On Feb 18, 2008, at 10:28 PM, Juergen Bosch wrote:
Chavas Leo wrote:
Dear Sun --
I want to check the conformation of one important amino acid in
the structure by looking the difference density map. Should I just
omit that amino acid in the refinement or should I also omit its
flanking amino acids? Which one is better?
The real expert will talk better than me, but I'd go for removing
1-2 additional residues around your target. Personal preferences
though... Depends on your resolution as well. If at low resolution
you remove 3 residues, you might have all of them gone for good, so
the target would be enough...
And then in addition running a composite omit map with CNS.
Good luck,
Jürgen
HTH
Kind regards.
Leo
------------------------------------------------------------
Chavas Leonard, Ph.D.
Research Associate
------------------------------------------------------------
Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
Oxford Road
Manchester Lancashire
M13 9PT
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Tel: +44(0)161-275-1586
e-mail: [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]
>
--
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
Miles Pufall
Postdoctoral Scholar
Yamamoto Lab
UC San Francisco
Cellular and Molecular Pharmacology
Mail Stop 2280
600 16th Street, Genentech Hall S-574
San Francisco, California 94158-2517
(415)476-4480
