[phenixbb] refinement of N-glycosylation

[Ling Qin]

Dear Georg,

Maybe you need to use quotation marks? I also have n-glycosylation and I in
my .eff file there is:

}
apply_cif_link {
data_link = "NAG-ASN"
residue_selection_1 = "chain A and resname NAG and resid XXX"
residue_selection_2 = "chain A and resname ASN and resid XXX"
}

Hope this is useful. Please correct me if I am wrong.

Ling


On Wed, Feb 24, 2010 at 1:13 PM, Georg Mlynek <georg.mlynek at univie.ac.at>wrote:

>  Dear All,
>
>
>
> I´m quite new to crystallography and I´m refining a structure with
> ASN-NAG-NAG-BMA attached and already got help from Blaine who told me how to
> do it, but I´m making a small mistake somewhere and can´t figure out what
> I´m doing wrong. Must be just one paranthesis or so, I guess.
>
> In command line just for testing I put:
>
> phenix.refine refine_data.mtz refine_1-coot-1FrenumberedGlu.pdb
> cif_link.params BMA.cif strategy=individual_sites+individual_adp
> main.number_of_macro_cycles=2 --overwrite
>
>
>
> where I put in cif_link.params as suggested in the mailing list
> http://www.phenix-online.org/pipermail/phenixbb/2009-November/002837.htmlwith and without paranthesis at the beginning
>
>
>
> }
>
>      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
>
>      }
>
>      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
>
>      }
>
>      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
>
>      }
>
>      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
>
>
>
> and suggested by Blaine with and without paranthesis at the beginning
>
>
>
> 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
>
>
>
> I see in the .geo file that the residues are not bonded, and also in the
> .eff file that these lines are not added there, which should be done I
> guess, I put the info also direct into the .def file but I get the same
> problem?
>
>
>
> By the way it shouldn´t matter which name I give to this file as long as
> the extension is correct?
>
>
>
> Thank you very much and all the best, Georg.
>
>
>
>
>
>
>
> -----Ursprüngliche Nachricht-----
> Von: phenixbb-bounces at phenix-online.org [mailto:
> phenixbb-bounces at phenix-online.org] Im Auftrag von Ursula Schulze-Gahmen
> Gesendet: Dienstag, 23. Februar 2010 19:20
> An: phenixbb at phenix-online.org
> Betreff: [phenixbb] weights optimization, add hydrogens
>
>
>
> I am refining a 2.0 A structure in Phenix using mostly the graphical
>
> interface. The maps are very good and the R factors are low
>
> (0.208/0.173). But the geometry is not so great with bond deviations of
>
> 0.208 and Angle deviations of 1.85.  What is the best thing to do to try
>
> to improve the geometry. Should I try to optimize the weights?
>
>
>
> The other question is about adding hydrogens to the model. I did add
>
> them in a previous refinement cycle. After rebuilding the model in coot,
>
> most of the model still has the hydrogens in the input file for the next
>
> refinement cycle, but some residues and waters don't have hydrogens.
>
> When I tried to add hydrogens again to the model, I got an error message
>
> about atoms being to close. Does Phenix know where to add hydrogens if
>
> the input model has already hydroegns on many residues?
>
>
>
>
>
> Thanks
>
>
>
> Ursula
>
>
>
> --
>
> Ursula Schulze-Gahmen, PhD.
>
> QB3, Tjian Lab
>
> MCB, 16 Barker Hall #3204
>
> University of California Berkeley
>
> Berkeley, CA 94720-3204
>
> Phone: (510) 642 8258
>
> uschulze-gahmen at lbl.gov
>
>
>
>
>
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>
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>
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>
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>
>
>
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