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
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Faculty of Life Sciences
The University of Manchester
The Michael Smith Building
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Manchester Lancashire
M13 9PT
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Tel: +44(0)161-275-1586
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--
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
