[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
> 
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
> 
> 




More information about the phenixbb mailing list