Re: [Jmol-users] adding hydrogens (Was: loading jmol file from open babel)

[Egon W. <e.w...@sc...>]

On Tuesday 30 January 2007, Francesco Pietra wrote:
> Let me say that a package dealing with molecules that
> does not place hydrogens correctly is of no use
> professionally. I must add that I am strongly
> disappointed, and back to my old MM package, which
> places the hydrogens correctly, like the nonvolatiles.
> How do you start a quantum mechanical computation with
> hydrogens not at their due place?

Dear Francesco,

It suprises me and I am sorry to hear that Jmol disappoints you.
Jmol is not a MM package, it is a visualizer, and I guess you gave it a try 
because Jmol's rendering engine compares quite favorable with several of the 
MM packages.

I am suprised that your MM package is able to sprout hydrogens correctly for 
PDB files, while these quite often contain imcomplete information on where to 
actually put those hydrogens; I refer to WhatCheck to see what problems 
normally occur in hydrogen locations in PDB files.

Moreover, Jmol does not incorrectly place hydrogens! It does not sprout 
hydrogen at all. Sprouting hydrogens in PDB entries is tricky business and is 
difficult to automate anyway. Therefore, I believe it is an excellent choice 
of Jmol to not provide this, as the goal of Jmol is visualisation, not a 
being a general purpose chemoinformatics toolkit. I refer to my other reply 
in this thread on why I think Jmol should not add this feature.

Finally, I would like to ask your attention for Bioclipse, which integrates 
Jmol, the CDK, BioJava, Rhino for JavaScripting, and which people have been 
extended for use in MM. Maybe that might meet your expectations.

Kind regards,

Egon Willighagen

-- 
e.w...@sc...
Cologne University Bioinformatics Center (CUBIC)
Blog: http://chem-bla-ics.blogspot.com/
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