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: [email protected] [mailto:[email protected]] Im Auftrag von Ursula Schulze-Gahmen Gesendet: Dienstag, 23. Februar 2010 19:20 An: [email protected] 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 [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb