[phenixbb] NAG-NAG description
Jonathan Elegheert
jonathan.elegheert at ugent.be
Tue Jun 1 05:18:00 PDT 2010
Hi Chris,
Your selection is 'empty' because your NAG is not resid 122 but 834.
Your ASN has resid 122.
You'll have to come to something like this; this correctly makes the
connections you want;
apply_cif_link {
data_link = "NAG-ASN"
residue_selection_1 = "chain A and resname NAG and resid 834"
residue_selection_2 = "chain A and resname ASN and resid 122"
}
apply_cif_link {
data_link = "BETA1-4"
residue_selection_1 = "chain A and resname NAG and resid 835"
residue_selection_2 = "chain A and resname NAG and resid 834"
}
HTH
Jonathan Elegheert
Ghent University
Op 01/06/10 13:44, Chris Ulens schreef:
> 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: 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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