<div dir="ltr">On Thu, Feb 6, 2014 at 1:07 PM, Edward A. Berry <span dir="ltr"><<a href="mailto:BerryE@upstate.edu" target="_blank">BerryE@upstate.edu</a>></span> wrote:<div class="gmail_extra"><div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Maybe a specialized tool like phenix.refine is safest!</blockquote><div><br></div><div>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.</div>
<div><br></div><div>For the record, I had to add parentheses to get the egrep command to work on my Mac:</div><div><br></div><div>egrep -v '^(ATOM|HETATM).*H$' m.pdb</div><div><br></div><div>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).</div>
<div><br></div><div>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.</div>
<div><br></div><div>-Nat</div></div></div></div>