On Thu, Feb 6, 2014 at 1:07 PM, Edward A. Berry <BerryE@upstate.edu> wrote:
Maybe a specialized tool like phenix.refine is safest!

At the risk of sounding like a broken record again: Unix shell tricks are great *if you already know how to use these tools* and have a detailed knowledge of the PDB format specification.  For everyone else, I do not recommend trying to edit models with anything other than a tool specifically designed for this purpose.  This is going to be especially important as the field slowly migrates to mmCIF.

For the record, I had to add parentheses to get the egrep command to work on my Mac:

egrep -v '^(ATOM|HETATM).*H$' m.pdb

which does the job.  But I do not think this solution is preferable to using phenix.reduce or phenix.pdbtools (or any number of other utilities).

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.

-Nat