[phenixbb] how to remove hydrogen from pdb

Tim Gruene tg at shelx.uni-ac.gwdg.de
Fri Feb 7 01:16:00 PST 2014

Hash: SHA1

Hi Nat,

On 02/06/2014 10:26 PM, Nathaniel Echols wrote:
> 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.

some time ago (about 6 months), Eugene Krissinel sported a similar
argument together with the statement that if a program does not exist
to do a particular job, it was the developers' task to fix it. At that
time I described a problem a student of mine had in data mining, but I
never received a response. I am glad somebody else here wrote a little
script to sort out the problem, because the numbers were important.
With the warning above and the implicit concept to wait for
developers, I still would not know. So I am happy about the
availability and possibility to use scripting to push my research
forward and not having to wait for someone to adjust my ideas to some API.


P.S.: I checked the command on some output from phenix and noticed
that the element type correctly is the last character of the line.
Some (older) PDB files from the PDB show two blank spaces, the the
regular expression does not work.

> 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
> _______________________________________________ phenixbb mailing
> list phenixbb at phenix-online.org 
> http://phenix-online.org/mailman/listinfo/phenixbb

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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