[phenixbb] automatic linking vs .params file; hydrogens

Georg Mlynek georg.mlynek at univie.ac.at
Tue Jun 17 16:47:12 PDT 2014

Dear phenix-development Team,

when is it advantageous to use automatic linking over supplying a .params file with the link parameters defined to refine links?

I thought that automatic linking will recognize the kind of link by itself and then look for the restraints itself. But it seems not to do,
because it is not complaining that there are still hydrogens in the sugar moeity which should not be there after the link has formed.

This brings me to my second questions. Is there a way to automatically remove the hydrogens which should not be there anymore after the bond has formed.  Or tell reduce that it should not add hydrogens at the link?

Thanks in advance.

Best Regards

    Automatic linking

phenix.refine has an automatic option for generating links /within the 
same chain/. It will look for carbohydrate links, both within the sugar 
polymer and linking to the protein. Covalent bonded ligands can also be 
linked with this option.

automatic_linking.link_all = True

There are a number of parameters that allow the tailoring of the various 
bond class cutoffs.

automatic_linking {
   metal_coordination_cutoff = 3.5
   amino_acid_bond_cutoff = 1.9
   rna_dna_bond_cutoff = 3.5
   inter_residue_bond_cutoff = 2.5
   carbohydrate_bond_cutoff = 1.99

There are also options within the automatic_linking scope for various 
bond length cutoffs.

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