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@phenix-online.org [mailto:phenixbb-bounces@phenix-online.org] Im Auftrag von Ursula Schulze-Gahmen
Gesendet: Dienstag, 23. Februar 2010 19:20
An: phenixbb@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
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