Dear Damien, Let me make a guess: You have the BETA1-4 linkages in the wrong order. If you look in the mon_lib_list.cif file, you can find the line where it says: BETA1-4 1 O4 2 C1 single 1.439 0.020 which tells me that the residue to be defined (residue_selection_1) ought to be the atom atom connecting with the O4 atom (the inner glycan) and the second residue is the one with the C1 atom (the outer glycan). So try switching residue_selection_1 and _2 for your BETA1-4 linkages. I know you are probably thinking BETA1-4 should go 1 to 4, but that is not how it is defined in the monomer library. By the way, your NAG-ASN linkages do look correct, and you have the correct anomers for beta-mannose (BMA) and alpha-mannose (MAN), which is where most people seem to get stuck. One stylistic question I have for you is, why are you naming your protein and glycans with different chain IDs; aren't they actually covalently linked? There apparently is no right way for numbering glycan residues, and everybody seems to be do a different thing... Good luck, Engin On 2/28/11 6:39 PM, Damian Ekiert wrote:
Sorry to bring up an old topic again but I can't find any documentation of glycan refinement on the Phenix website and previous threads don't seem to answer my question.
I am refining a structure with N-linked glycans. I have inserted several "apply_cif_link" records to my .eff file to define the glycan topologies (see below) and fed in a cif file for BMA. After fiddling for quite some time now, I have managed to get around all the error messages people have described previously to disappear. Yet, 1) none of my linkages appear to be enforced and 2) even the restraints on the individual sugars appear to be unenforced (or at least, insufficiently so). For example, some rings are rendered almost flat, or flipped into boat or otherwise distorted conformations, and glycosidic bonds stretch to>2 A.
No obvious signs of trouble in the log file, running the latest version (1.7, also tried 1.6.4), but my glycans look terrible (despite some of the best density I have ever seen! :-) )
Any suggestions would be appreciated!
Thanks,
Damian Ekiert
From my .eff file:
apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain X and resname NAG and resid 401 residue_selection_2 = chain A and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Y and resname NAG and resid 401 residue_selection_2 = chain C and resname ASN and resid 91 } apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain Z and resname NAG and resid 401 residue_selection_2 = chain E and resname ASN and resid 91 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain X and resname NAG and resid 402 residue_selection_2 = chain X and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname NAG and resid 402 residue_selection_2 = chain Y and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Z and resname NAG and resid 402 residue_selection_2 = chain Z and resname NAG and resid 401 } apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain Y and resname BMA and resid 403 residue_selection_2 = chain Y and resname NAG and resid 402 } apply_cif_link { data_link = ALPHA1-3 residue_selection_1 = chain Y and resname MAN and resid 404 residue_selection_2 = chain Y and resname BMA and resid 403 } _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111