[phenixbb] how to remove hydrogen from pdb

Nathaniel Echols nechols at lbl.gov
Thu Feb 6 13:26:43 PST 2014

On Thu, Feb 6, 2014 at 1:07 PM, Edward A. Berry <BerryE at 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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20140206/bafd5e44/attachment.htm>

More information about the phenixbb mailing list