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Re: [ccp4bb] Check the conformation of one important amino acid |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 19 February 2008Subject: Re: Check the conformation of one important amino acid From: Miles Pufall mpufall {- at -} CMP {- dot -} UCSF {- dot -} EDU Date: 2008-02-19 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 >> ------------------------------------------------------------ >> Tel: +44(0)161-275-1586 >> e-mail: Leonard.Chavas@manchester.ac.uk >> > >> >> > > > -- > 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 CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 19 February 2008 |
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