[phenixbb] N-linked glycans in phenix.refine

Jose Casasnovas jcasasnovas at cnb.csic.es
Wed Sep 30 03:41:15 PDT 2009


Thanks so much for the update.  You were right.
Now I have another problem, maybe you know.  I am 
using a NAG without the O1 and the program is trying to delete and stop

RuntimeError: delete_atom_in_place: unknown atom_id: O1

Do you know how to avoid this?

Jose




At 20:22 29/09/2009, you wrote:
>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
>
>_______________________________________________
>phenixbb mailing list
>phenixbb at phenix-online.org
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