[phenixbb] refinement of N-glycosylation

Georg Mlynek georg.mlynek at univie.ac.at
Wed Feb 24 13:13:52 PST 2010


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.html
with 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

 

 

_______________________________________________

phenixbb mailing list

phenixbb at phenix-online.org

http://phenix-online.org/mailman/listinfo/phenixbb

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100224/81c70a8e/attachment-0003.htm>


More information about the phenixbb mailing list