[phenixbb] hydrogen nomenclature

Nathaniel Echols nechols at lbl.gov
Tue Oct 23 10:08:36 PDT 2012

On Tue, Oct 23, 2012 at 9:25 AM, Jeff Headd <jjheadd at lbl.gov> wrote:
> You are right that hydrogen nomenclature can be a real problem. While the
> monomer library does use the older naming convention

Not in ccp4 6.3.0, it doesn't - HB2 and HB3 are used.  Patrick, where
is your CCP4 monomer library coming from?  It sounds like it may be
out of date.

Oddly, $PHENIX/chem_data/geostd/l/data_LEU.cif uses HB1/HB2, although
if you use Reduce/phenix.ready_set to add hydrogens, and refine in
Phenix, I think they should still have the v. 3 labels.


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