[phenixbb] Another dictionary question...
Schubert, Carsten [PRDUS]
CSCHUBER at prdus.jnj.com
Fri Aug 8 07:41:47 PDT 2008
Simon,
I am not familiar with the mechanism behind cif-links, but when I refined NAG-aa complexes I just defined the relevant bonds and angles under geometry_restraints.edits.bond or .angle . You need to select individual atoms in this case though.
I can dig out an old .def file and send it to you if you get stuck.
Carsten
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org]On Behalf Of Simon Kolstoe
> Sent: Friday, August 08, 2008 9:46 AM
> To: PHENIX user mailing list
> Subject: [phenixbb] Another dictionary question...
>
>
> Sorry for one more question:
>
> I am now trying to build in some sugar NAG residues that are
> N-linked
> to an Asn. I've used the parameter file below, and the first time
> phenx.refine ran perfectly. However after a bit of rebuilding I get
> the following error:
>
> result.delete_atom_in_place(mod_atom.atom_id)
> File "/usr/local/phenix-1.3-rc4/mmtbx/mmtbx/monomer_library/
> cif_types.py", line 244, in delete_atom_in_place
> raise RuntimeError("delete_atom_in_place: unknown
> atom_id: %s" %
> atom_id)
> RuntimeError: delete_atom_in_place: unknown atom_id: O1
>
> I think this is referring to the O1 atom of the NAG sugar which the
> program had deleted the first time it ran in order to form the bond
> with the Asn. Is there any way of stopping phenix trying to delete
> this atom again?
>
> Thanks,
>
> Simon
>
> My cif_links.param file that is incorporated into my .def
> file second
> time round:
>
> refinement.pdb_interpretation.apply_cif_link {
> data_link = NAG-ASN
> residue_selection_1 = chain A and resname NAG and resid 207
> residue_selection_2 = chain A and resname ASN and resid 32
>
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