[phenixbb] weights optimization, add hydrogens
Schubert, Carsten [PRDUS]
CSCHUBER at its.jnj.com
Tue Feb 23 12:58:46 PST 2010
phenix.reduce does generate "old-style" hydrogens if the proper options are used, ie.
phenix.reduce in.pdb -BUILD -OLDpdb > out.pdb
The hydrogens are compatible with coot v0.5 and v0.6 for hydrogens attached to standard protein residues.
I agree that stripping the hydrogens and regeneration after rebuilding/mutation and prior to refinement is the safest path for now until better support is implemented.
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org [mailto:phenixbb-
> bounces at phenix-online.org] On Behalf Of Christian Roth
> Sent: Tuesday, February 23, 2010 5:26 PM
> To: phenixbb at phenix-online.org
> Subject: Re: [phenixbb] weights optimization, add hydrogens
> Dear Ursula,
> I usually remove the hydrogens and add them again in the next
> refinement cycle.
> Something strange happens If you simply try to update the hydrogens.
> I use phenix.pdbtools to remove the hydrogens.
> Also Coot cannot handle the hydrogens properly in real space
> refinement. At
> least in my version the Hydroges from the refined residue got to
> everywhers in
> any density.
> Best regards
> Am Dienstag 23 Februar 2010 19:33:03 schrieb Nathaniel Echols:
> > On Feb 23, 2010, at 10:19 AM, Ursula Schulze-Gahmen wrote:
> > > The other question is about adding hydrogens to the model. I did
> add them
> > > in a previous refinement cycle. After rebuilding the model in coot,
> > > of the model still has the hydrogens in the input file for the next
> > > refinement cycle, but some residues and waters don't have
> hydrogens. When
> > > I tried to add hydrogens again to the model, I got an error message
> > > atoms being to close. Does Phenix know where to add hydrogens if
> > > input model has already hydroegns on many residues?
> > In theory it should, but the underlying problem is almost certainly
> > incompatible names for hydrogen atoms, which will appear invisible
> > Reduce (the program that adds them). This usually results from
> > between programs that have different conventions for hydrogen naming
> > Coot and Phenix), depending on which version of the PDB format they
> > (Phenix uses PDB v3.2, which is very new.)
> > Would you mind sending me (not the list!) the PDB file so I can
> > double-check this? Unfortunately I don't have any suggestions for
> how to
> > fix this other than wiping out the old hydrogen atoms (I like PyMOL
> > this: "remove elem h"). Since this keeps coming up, we'll add an
> > to the GUI to erase old hydrogen atoms before running the automatic
> > addition.
> > thanks,
> > Nat
> > -------------------
> > Nathaniel Echols
> > Lawrence Berkeley Lab
> > 510-486-5136
> > NEchols at lbl.gov
> > _______________________________________________
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> > phenixbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/phenixbb
> Christian Roth
> Institut für Bioanalytische Chemie
> Biotechnologisch-Biomedizinisches Zentrum
> Fakultät für Chemie und Mineralogie
> Universität Leipzig
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> 04103 Leipzig
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