[phenixbb] refinement of N-glycosylation

Georg Mlynek georg.mlynek at univie.ac.at
Thu Feb 25 13:35:47 PST 2010


Dear All, 


1)      thank you very much for the help with the glycosylations. Blaine was
right yesterday that I just forgot to set the last brace. As this is also a
common question, I thought maybe the “manual” I wrote now for this issue can
be put also in the FAQs .(lots I wrote is just pasted from the manual.



1)  check if you take the right sugars. BMA is not same as MAN for example.
good papers are:


pdb-care (PDB CArbohydrate REsidue check): a program to support annotation
of complex carbohydrate structures in PDB files Thomas Lütteke and Claus-W
von der Lieth

Data mining the protein data bank: automatic detection and assignment of
carbohydrate structures Thomas Lütteke, Martin Frank and Claus-W. von der


2) check which links you need. There are already lots of predefined links in
phenix stored in the file  mon_lib_list.cif


The full path to this file can be obtained with the command:


% phenix.where_mon_lib_list_cif


All apply_cif_modification and apply_cif_link definitions will be included
into the .def files. I.e. it is not necessary to specify the definitions
again if further refinement runs are started with .def files. Note that all
LINK, SSBOND, HYDBND, SLTBRG and CISPEP records in the input PDB files are


3) Create a file which you can call whatever you want even the extension
doesn't matter. E.g.: cif_link.params


Put in this file your links: (Which Atom of residue1 will be connected to
which Atom in residue2 is already defined in mon_lib_list.cif)




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



4) run % phenix.refine model.pdb data.hkl cif_link.params



5)Trouble shooting


a)run iotbx.phil cif_link.params   (this checks if the syntax is right)


b) check .eff file the links should be added there. You can also check the .
geo file if you see anything strange.


c)Having unknown to phenix.refine item in PDB file (novel ligand, etc...
(BMA is also not there) ). phenix.refine uses the CCP4 Monomer Library as
the source of stereochemical information for building geometry restraints
and reporting statistics. If phenix.refine is unable to match an item in
input PDB file against the Monomer Library it will stop with "Sorry" message
explaining what to do and listing the problem atoms. If this happened, it is
necessary to obtain a cif file (parameter file, describing unknown molecule)
by either making it manually or having eLBOW program to generate it:


phenix.elbow model.pdb --do-all --output=all_ligands


this will ask eLBOW to inspect the model_new.pdb file, find all unknown
items in it and create one cif file for them all_ligands.cif. Alternatively,
one can specify a three-letters name for the unknown residue:


phenix.elbow model.pdb --residue=MAN --output=man


!Check the file if everything is ok!


Once the cif file is created, the new run of phenix.refine will be:


phenix.refine model.pdb data.pdb man.cif


Consult eLBOW documentation for more details. Check the file





2)      From the command line everything is perfect now, but as I also want
to know how to do this with the gui (version 1.6-289), I added the files
BMA.cif file and the apply_cif_link.params together with my coordinates and
the mtz in the Input files. But I get following error message:


Screenshot-PHENIX errorcif.png


Is this a Bug?


Thanks again and kind regards Georg.




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