[phenixbb] Question about adding hydrogrens with reduce --parameters for phenix.refine
Schubert, Carsten [PRDUS]
CSCHUBER at prdus.jnj.com
Thu Dec 6 12:12:38 PST 2007
Upgrading to rc6 fixed the reduce issue.
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org]On Behalf Of Schubert,
> Carsten [PRDUS]
> Sent: Thursday, December 06, 2007 2:27 PM
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] Question about adding hydrogrens with reduce
> --parameters for phenix.refine
> 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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