[phenixbb] NAG-NAG description

Chris Ulens chris.ulens at med.kuleuven.be
Tue Jun 1 04:44:18 PDT 2010


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

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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.
>
>
> -----Urspr?ngliche Nachricht-----
> Von: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org] 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   chris.ulens at med.kuleuven.be
> t    +32 16 345812
> f    +32 16 345699
> w   http://www.xtal.be
>
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