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 glycosidic_bond_beta1-4

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.
data_link_BETA1-4 # loop_ _chem_link_bond.link_id _chem_link_bond.atom_1_comp_id _chem_link_bond.atom_id_1 _chem_link_bond.atom_2_comp_id _chem_link_bond.atom_id_2 _chem_link_bond.type _chem_link_bond.value_dist _chem_link_bond.value_dist_esd 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).

Engin

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
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Engin Özkan 
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