Re: [Jmol-users] Protein Hydrogen Bonds again

[David L. <d.l...@bi...>]

Thanks for the response to my message. I've been tied up with  
something and now it's quite late in Europe so I'll just send a brief  
reply to a couple of points and any further info later.

1. My interest is only in proteins where the hydrogens have been  
added. The database of the proteins I wish to display is  
predominantly the Richardson 500, where the resolution is never more  
than 2 angstroms, all the hydrogens have been added, and ambiguous  
residues checked manually. We are only interested in displaying H- 
bonds we are pretty sure about.

2. Our database is of hydrogen-bonded small 3D protein motifs, and  
includes all the H-bonds in the proteins. These have been derived  
using Janet Thornton's HBPlus program. However this is not public  
domain. The program program from the student many years ago is first  
rate. It was initially written by a lecturer in computing science  
here in Glasgow and the student made modifications. This was the  
brightest PhD student my colleague ever had. I don't think there is  
any question about the quality of the program.

The suggestion of writing extra scripts seems unattractive at first  
sight. At the moment, after a search I am allowing a user to fire up  
Jmol showing the motifs in the context of the protein all generated  
on the fly. It's tricky enough to generate javascript controls for a  
particular situation in the context of the pdb file and the residues  
in the motifs. I haven't done anything with Jmol for two years (my  
web app uses 10.2) so perhaps I am overestimating the difficulty of   
the problem.

David

PS The web application I am using can be found at http:// 
motif.gla.ac.uk/motif/index.html. To see what I mean:

->Motifs in a Protein
->eg 1BX4 and Asx Turn
->3D
->Single Motif Display
->Motif 1
->Hydrogen Bonds on (nothing happens)
I would like to display the H-bond from Asn to main-chain NH.
If you choose Beta Turn for the same protein, the main-chain - main- 
chain H-bonds can be displayed.

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Dr. David P. Leader, Faculty of Biomedical & Life Sciences,
University of Glasgow, Glasgow G12 8QQ, UK
Phone: +44 (0)141 330 5905
http://doolittle.ibls.gla.ac.uk/leader

The University of Glasgow, charity number SC004401
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