Subject: Summary: software to add Hydrogens to proteins.

From: Mark Thompson <[email-masked]>
Date: Sun, 24 Aug 1997 17:05:59 -0700 (PDT)

Previously, I requested:

> I need to find software that will add
> hydrogens to proteins structures in
> PDB format. It must run on a PC (win95 or NT).

Here is a brief summary of  the responses I received.

I downloaded MSI's WebLab viewer (option B, below) and
really like it.  I still have not tried the other
options.

Thanks again to all who responded.  Your suggestions
were very helpful.

Mark Thompson

A).
Rick Ornstein had a program called Network.  It worked on Biosym car files; so
maybe you could do a translation.  I don't know if it is still maintained by
his group.  Also, it was written for UNIX but could probably be ported to NT.

B)
Try WebLab Viewer 2.0 - available free from MSI at
    http://www.msi.com/weblab/viewer/index.htm

C)
If you have a good Kekule structure available, then PCMODEL (Serena
Software...812-3330823/[email-masked]) should be able to do it.

D)
Dear Mark, Babel (freeware) can add/subtract H atoms to several types of 
files, enclosed PDB files. I've not the exact address of it in mind while 
I'm writing but you may find a link to it in our software page at
http://antas.agraria.uniss.it

E)
This is a very basic feature that probably isn't highlighted because just
about every program can do it.  Chem3D, Macromodel, and Hyperchem are among
the three most-often-mentioned programs on this list, I think.  All of them
can do what you describe.  For more information, see (in order):

http://www.camsoft.com
http://www.columbia.edu/cu/chemistry/mmod/mmod.html
http://www.hyper.com

F)
Check out the Molecular Modelling Toolkit at

    http://starship.skyport.net/crew/hinsen/mmtk.html

It has everything you need to addd hydrogens in reasonable (but not
necessarily energy-minimized) positions to proteins. It's free and
should run on Win95 and NT (but not DOS or Win 3.1 - it needs long
file names), although I have tested it only on Unix systems.