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

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Thu Dec 6 11:26:30 PST 2007


I am using phenix rc5 and reduce in that version. Funny, it appears I just upgraded, tough to keep up with you guys. I'll upgrade to rc6 and see if this problem still persists



> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org]On Behalf Of Ralf W.
> Grosse-Kunstleve
> Sent: Thursday, December 06, 2007 2:15 PM
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] Question about adding hydrogrens with 
> reduce --
> parameters for phenix.refine
> 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
>   phenix.version
> 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).
> Ralf
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