[phenixbb] links in phenix summary

Christian Roth christian.roth at bbz.uni-leipzig.de
Mon Jan 30 00:36:26 PST 2012

Dear all,

thanks to the phenix team which helped me a lot to resolve all issues 
regarding the correct link definitions. 

I have summarised a few things which one might consider if nonstandard links 
are necessary. 

Try phenix ready set to get your links out of the pdb. Do not forget to change 
the possible LINKR to LINK!
Inspect the links and decide if they are useful!
Peptide links are automatically incorporated if residues are close (inspect 
geo file)
Non standard peptide links could be created using using an now available alpha 
release script:

elbow.ligand_linking model.pdb

Inspect the generated cif file and correct angles and incorporate dihedrals and 
so on if necessary.

Sugar links which exists in the mon_lib.cif should be incorporated using the 
apply_cif link option like
refinement.pdb_interpretation.apply_cif_link {
     data_link = ALPHA1-4
     residue_selection_1 = chain B and resname GLC and resseq    1
     residue_selection_2 = chain B and resname GLC and resseq    2
According to the link definition the C1 oxygen of the following sugar with the 
higher number must be removed.
The automatic incorporation of sugar links will be probably soon available in 
phenix. Nigel is already working on this. 
If one want use hydrogens in the refinement, they have to be added previously 
with ready_set and afterwards the OH4 sugar hydrogen has to be removed before 
the refinement. 

For links with symmetry related atoms the symmetry operator must be included 
in a custom bond definition
efinement.geometry_restraints.edits {
  bond {
    action = *add delete change
    atom_selection_1 = chain A and resname HEM and resid 154 and name FE
    atom_selection_2 = chain A and resname MTO and resid 155 and name O
    symmetry_operation = -x,y,-z
    distance_ideal = 2.2
    sigma = 0.01
The operator can be obtained using 

iotbx.show_distances your.pdb > all_distances

Search for keyword "sym"
or from Coot clicking on the symm option. Coot print out the operator and the 
translation term separately. Both has to be merged in the  final operator used 
in phenix!


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