Thanks for the feedback.
I would like to refine a NAG-NAG chain attached to residue Asn122 in my structure. There are 5 identical subunits.
Could you verify my .params file?
I get the following error:
Empty atom selection
refinement.pdb_interpretation.apply_cif_link.residue_selection_1="chain A and resname NAG and resid 122"

Thanks.
-Chris




On 31 May 2010, at 21:34, Georg Mlynek wrote:

Dear Chris, this did it for me.


Create a file which you can call whatever you want even the extension
doesn't matter. E.g.: cif_link.params

Put in this file your links: (Which Atom of residue1 will be connected to
which Atom in residue2 is already defined in mon_lib_list.cif)



refinement.pdb_interpretation.apply_cif_link {
      data_link = NAG-ASN
      residue_selection_1 = chain A and resname NAG and resid 500
      residue_selection_2 = chain A and resname ASN and resid 297
    }
    refinement.pdb_interpretation.apply_cif_link {
      data_link = BETA1-4
      residue_selection_1 = chain A and resname NAG and resid 500
      residue_selection_2 = chain A and resname NAG and resid 501
    }
    refinement.pdb_interpretation.apply_cif_link {
      data_link = BETA1-4
      residue_selection_1 = chain A and resname NAG and resid 501
      residue_selection_2 = chain A and resname BMA and resid 502
    }
    refinement.pdb_interpretation.apply_cif_link {
      data_link = ALPHA1-3.

      residue_selection_1 = chain A and resname BMA and resid 502
      residue_selection_2 = chain A and resname MAN and resid 503
    }

4) add this file in the GUI


Or run % phenix.refine model.pdb data.hkl cif_link.params


5)Trouble shooting

a)run iotbx.phil cif_link.params   (this checks if the syntax is right)

b) check .eff file the links should be added there. You can also check the .
geo file if you see anything strange.

c)Having unknown to phenix.refine item in PDB file (novel ligand, etc...
(BMA is also not there) ). phenix.refine uses the CCP4 Monomer Library as
the source of stereochemical information for building geometry restraints
and reporting statistics. If phenix.refine is unable to match an item in
input PDB file against the Monomer Library it will stop with "Sorry" message
explaining what to do and listing the problem atoms. If this happened, it is
necessary to obtain a cif file (parameter file, describing unknown molecule)
by either making it manually or having eLBOW program to generate it:

phenix.elbow model.pdb --do-all --output=all_ligands

this will ask eLBOW to inspect the model_new.pdb file, find all unknown
items in it and create one cif file for them all_ligands.cif. Alternatively,
one can specify a three-letters name for the unknown residue:

phenix.elbow model.pdb --residue=MAN --output=man

!Check the file if everything is ok!


Please correct if this is not ok, or there is an easier way now.

Kind regards George.


-----Ursprüngliche Nachricht-----
Von: [email protected]
[mailto:[email protected]] Im Auftrag von Chris Ulens
Gesendet: Monday, May 31, 2010 9:14 PM
An: PHENIX user mailing list
Betreff: Re: [phenixbb] NAG-NAG description

Dear glycobiologists and phenixfriends.

I am trying to refine a NAG-NAG chain attached to an Asn122 in my
(pentameric) structure.
What is the proper description in the cif_link.params that is the
equivalent of the pdb description pasted below that phenix so kindly
ignores?
Also, what is the proper way to define the cif_link.params file in the
GUI?

Thank you.
-Chris


LINK         ND2 ASN A 122                 C1  NAG A 834     1555
1555  1.37
LINK         O4  NAG A 834                 C1  NAG A 835     1555
1555  1.43
LINK         ND2 ASN B 122                 C1  NAG B 834     1555
1555  1.37
LINK         O4  NAG B 834                 C1  NAG B 835     1555
1555  1.43
LINK         ND2 ASN C 122                 C1  NAG C 834     1555
1555  1.37
LINK         O4  NAG C 834                 C1  NAG C 835     1555
1555  1.43
LINK         ND2 ASN D 122                 C1  NAG D 834     1555
1555  1.37
LINK         O4  NAG D 834                 C1  NAG D 835     1555
1555  1.43
LINK         ND2 ASN E 122                 C1  NAG E 834     1555
1555  1.37
LINK         O4  NAG E 834                 C1  NAG E 835     1555
1555  1.43

---------------------------------------------------
Chris Ulens, Ph.D.
Lab of Structural Neurobiology
Department of Molecular Cell Biology
Campus Gasthuisberg, ON1
Herestraat 49, PB 601
B-3000 Leuven
Belgium
e   [email protected]
t    +32 16 345812
f    +32 16 345699
w   http://www.xtal.be

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