[phenixbb] links in phenix summary
christian.roth at bbz.uni-leipzig.de
Mon Jan 30 00:36:26 PST 2012
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
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
Non standard peptide links could be created using using an now available alpha
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
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
For links with symmetry related atoms the symmetry operator must be included
in a custom bond definition
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
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