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Dear Jose and Tirumala,<br>
<br>
If you read inside the file this command shows you:
phenix.where_mon_lib_list_cif, you can see<br>
<br>
<tt>BETA1-4 . DEL-HO4 pyranose . DEL-O1 pyranose<br>
glycosidic_bond_beta1-4</tt><br>
<br>
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.<br>
<tt><br>
data_link_BETA1-4<br>
#<br>
loop_<br>
_chem_link_bond.link_id<br>
_chem_link_bond.atom_1_comp_id<br>
_chem_link_bond.atom_id_1<br>
_chem_link_bond.atom_2_comp_id<br>
_chem_link_bond.atom_id_2<br>
_chem_link_bond.type<br>
_chem_link_bond.value_dist<br>
_chem_link_bond.value_dist_esd<br>
BETA1-4 1 O4 2 C1 single 1.439 0.020</tt><br>
<br>
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).<br>
<br>
Engin<br>
<br>
<br>
On 10/1/09 4:04 AM, Jose M Casasnovas wrote:
<blockquote cite="mid:20091001130436.zn9kvuweo88o0o40@webmail.csic.es"
type="cite">
<p>Dear Ralf.</p>
<p>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).<br>
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. <br>
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.</p>
<p>Thanks so much for your help and to all who sent comments and
suggestions.</p>
<p>Jose M Casasnovas<br>
-- <br>
Centro Nacional de Biotecnología (lab. B16)<br>
CSIC, Campus UAM<br>
Darwin 3<br>
28049 Madrid<br>
Spain<br>
Ph. 34 915854917(8)<br>
Fax. 34 915854506<br>
email: <a class="moz-txt-link-abbreviated" href="mailto:jcasasnovas@cnb.csic.es">jcasasnovas@cnb.csic.es</a></p>
<br>
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<br>
<br>
<pre class="moz-signature" cols="72">--
Engin Özkan
Post-doctoral Scholar
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
ph: (650)-498-7111</pre>
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