[Molvis-list] adding hydrogens to a pdb file

Elmar Krieger elmar at cmbi.ru.nl
Wed Jan 19 04:47:12 EST 2005

Hi Jeff,

> There used to be a WHAT IF web interface in which a user could submit a 
> PDB ID number and get back an "hadded.pdb" file with hydrogen atoms 
> added.  This site no longer exists, and the WHAT IF software is now only 
> available to those who purchase it for 500 Euros (at 
> http://swift.cmbi.kun.nl/whatif/).

The new URL for this server is http://swift.cmbi.kun.nl/WIWWWI/
(btw, the price of WHAT IF is still 250 EUR for the Linux version ;-).

If you want to work locally, you can also download YASARA View
( http://www.yasara.org/viewdl ), and click on Edit > Add > Hydrogens to all.
But only the WHAT IF server will do elaborate things like flipping Asn, Gln, His 
side-chains to optimize the hydrogen bonding network.


Elmar Krieger, PhD
YASARA Biosciences & CMBI Outstation Austria
Neue-Welt-Hoehe 13/b
A-8042 Graz

=WHAT IF YASARA knows the answer?!=
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