[phenixbb] how to remove hydrogen from pdb

Nathaniel Echols nechols at lbl.gov
Fri Feb 7 13:25:10 PST 2014

On Thu, Feb 6, 2014 at 1:26 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> A final note: in my experience, if you deposit a file containing hydrogens
> to the PDB, they're just going to delete them for you (whether you want
> this or not!), so it is not necessary to do any additional preparation.  In
> fact, I just did this last week, so we'll see what happens.

In confirmation of this, here's what the PDB annotator said:

"The H atoms in the coordinates all have zero occupancy, would you like to
remove them from the coordinates?"

Which obviously indicates a bug in phenix.refine (specifically the mmCIF
output - the PDB-format file is okay), but my point stands.

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