[phenixbb] weights optimization, add hydrogens

Nathaniel Echols NEchols at lbl.gov
Tue Feb 23 10:33:03 PST 2010

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 the 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 option to the GUI to erase old hydrogen atoms before running the automatic addition.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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