[phenixbb] Question about adding hydrogrens with reduce -- parameters for phenix.refine

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Dec 6 11:15:11 PST 2007

Hi Carsten,
> To my surprise it only applies hydrogens to a selected few residues.
That sounds like a bug. It should add almost all hydrogens, with the
few exceptions indicated in the -help output.
Which version of phenix is this? -- In newer versions you can run
to find out.
The version information shown at the beginning of the phenix.reduce
output would also be useful to know.
Are you adding the hydrogens to protein or rna/dna?

> If I would use another tool to generate the hydrogens, like
> CNS(X) or Maeastro, how compatible are the parameter files?

As of Sep this year phenix.refine should deal with any of the hydrogen
naming conventions (old pdb, new pdb, refmac, cns). This is for
standard protein and rna/dna. Ligands may require special attention,
e.g. a special parameter file (use phenix.elbow).


More information about the phenixbb mailing list