[phenixbb] N-linked glycans in phenix.refine

Engin Ozkan eozkan at stanford.edu
Tue Sep 29 11:22:50 PDT 2009


That's because there is no such data link as NAG-NAG-B-D. Instead, you 
should use a BETA1-4 link. This is similar to what CNS used, if you are 
familiar with that (I think it was B14 in CNS).
If you want to know where all the phenix link definitions are, type

phenix.where_mon_lib_list_cif

and read the file that's listed.

It is good to read this to know which residue selection is selection_1 
and which is selection_2. In it you'll see this or something like this.

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
loop_
_chem_link_angle.link_id
_chem_link_angle.atom_1_comp_id
_chem_link_angle.atom_id_1
_chem_link_angle.atom_2_comp_id
_chem_link_angle.atom_id_2
_chem_link_angle.atom_3_comp_id
_chem_link_angle.atom_id_3
_chem_link_angle.value_angle
_chem_link_angle.value_angle_esd
  BETA1-4  1 C4      1 O4      2 C1      108.700    3.000
  BETA1-4  1 O4      2 C1      2 O5      112.300    3.000
  BETA1-4  1 O4      2 C1      2 C2      109.470    3.000
  BETA1-4  1 O4      2 C1      2 H1      109.470    3.000
loop_
_chem_link_tor.link_id
_chem_link_tor.id
_chem_link_tor.atom_1_comp_id
_chem_link_tor.atom_id_1
_chem_link_tor.atom_2_comp_id
_chem_link_tor.atom_id_2
_chem_link_tor.atom_3_comp_id
_chem_link_tor.atom_id_3
_chem_link_tor.atom_4_comp_id
_chem_link_tor.atom_id_4
_chem_link_tor.value_angle
_chem_link_tor.value_angle_esd
_chem_link_tor.period
  BETA1-4  BETA_1   1 O4     2 C1     2 C2     2 C3        0.00  20.0 1
  BETA1-4  BETA_2   1 C4     1 O4     2 C1     2 C2        0.00  20.0 1
  BETA1-4  BETA_3   1 C3     1 C4     1 O4     2 C1        0.00  20.0 1
loop_
_chem_link_chir.link_id
_chem_link_chir.atom_centre_comp_id
_chem_link_chir.atom_id_centre
_chem_link_chir.atom_1_comp_id
_chem_link_chir.atom_id_1
_chem_link_chir.atom_2_comp_id
_chem_link_chir.atom_id_2
_chem_link_chir.atom_3_comp_id
_chem_link_chir.atom_id_3
_chem_link_chir.volume_sign
  BETA1-4    2 C1      1 O4      2 O5      2 C2      positiv

Engin


On 9/29/09 10:44 AM, Jose Casasnovas wrote:
> Dear Phenix users.
> I am trying to refine N-linked glycans in phenix.  The Asn-NAG link
> appears to be recognize by the program, but the NAG-NAG link is not.
> I guess the cif_link must be missing.
>
>
>    Monomer Library directory:
>       "/home/soft/phenix/phenix-1.4-3/ext_ref_files/mon_lib"
>     Total number of atoms: 8947
>     apply_cif_link:
>       data_link: NAG-ASN
>         mod_id_1: DEL-O1
>         mod_id_2: DEL-HD22
>       residue_selection_1: chain N and resname NAG and resid 5161
>       residue_selection_2: chain E and resname ASN and resid 516
>     apply_cif_link:
>       data_link: NAG-NAG-B-D
>
> Sorry: Missing CIF link: data_link_NAG-NAG-B-D
>     Please check for spelling errors or specify the file name
>     with the link as an additional argument.
>
> How can I get the required cif_link file and where to place it??
>
> Any suggestion.
>
> Thanks.
>
> Jose
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>    


-- 
Engin Özkan
Post-doctoral Scholar
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




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