[phenixbb] refining sugars
eozkan at stanford.edu
Thu Oct 1 08:22:07 PDT 2009
Dear Jose and Tirumala,
If you read inside the file this command shows you:
phenix.where_mon_lib_list_cif, you can see
BETA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose
which will tell you that in the BETA1-4 link description, the first
residue selection has the pyranose that loses its HO4 hydrogen, and the
second residue selection has the pyranose that loses the O1 oxygen.
BETA1-4 1 O4 2 C1 single 1.439 0.020
Also here, you can see that the first residue has the O4, and the second
has C1 that are making the beta 1-4 linkage. Or at least I find it out
that way. You may need further linkages and correct N-linked sugar names
that phenix provides cif files for (such as L-fucose and D-mannose,
which is apparently commonly misnamed in the pdb).
On 10/1/09 4:04 AM, Jose M Casasnovas wrote:
> Dear Ralf.
> I just solved the problem with the sugar refinement. Somehow the way
> the BETA1-4 cif defines the link is in the reverse order to the
> NAG-ASN cif link (at least to way I was used to do it).
> In the NAG-ASN cif, residue_selection_1 in the phenix.refine input
> must be the NAG and residue_selection_2 the ASN, such as I was used to
> do in CNS.
> However, the BETA1-4 cifs follows the opposite way:
> residue_selection_1 must be the first sugar residue (linked through
> O4) and residue_selection_2 the second sugar (linked through the C1),
> which is the most distant residue to the Asn.
> Thanks so much for your help and to all who sent comments and suggestions.
> Jose M Casasnovas
> Centro Nacional de Biotecnología (lab. B16)
> CSIC, Campus UAM
> Darwin 3
> 28049 Madrid
> Ph. 34 915854917(8)
> Fax. 34 915854506
> email: jcasasnovas at cnb.csic.es
> phenixbb mailing list
> phenixbb at phenix-online.org
Laboratory of K. Christopher Garcia
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
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