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. Cheers, Carsten
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Christian Roth Sent: Tuesday, February 23, 2010 5:26 PM To: [email protected] 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
Christian
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, most 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 about 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 to Reduce (the program that adds them). This usually results from switching between programs that have different conventions for hydrogen naming (e.g. Coot and Phenix), depending on which version of the PDB format they use. (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 for this: "remove elem h"). Since this keeps coming up, we'll add an
Am Dienstag 23 Februar 2010 19:33:03 schrieb Nathaniel Echols: the option
to the GUI to erase old hydrogen atoms before running the automatic addition.
thanks, Nat
------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
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-- Christian Roth Institut für Bioanalytische Chemie Biotechnologisch-Biomedizinisches Zentrum Fakultät für Chemie und Mineralogie Universität Leipzig Deutscher Platz 5 04103 Leipzig Telefon: +49 (0)341 97 31316 Fax: +49 (0)341 97 31319 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb