Thanks Tim and Miguel for your responses to my query about setting
one's own H-bonds. One thing I wrote was incorrect - the H-bonds are
not decided arbitrarily by the expert but by running the HBPlus
program on the pdb file. These are then stored in my MySQL database.
Thus, in the light of Miguel's comments about the hbonds being read
from the CONECT lines (why did they choose that weird spelling?) I
suppose I could programmatically rewrite all the 500 pdb files I'm
using (a student exercise for later I think), but for the moment I'll
follow Tim's suggestion of incorporating the donor and acceptor atoms
into a script after retrieving them on the fly. I'll contact him off
list, as he suggests, and report back to the list if and when the
thing is up and running.
David
--
_______________________________________________________________
David P.Leader, Biochemistry and Molecular Biology
Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK
Phone: +44 41 330-5905 http://doolittle.ibls.gla.ac.uk/leader
_______________________________________________________________
-------------------------------------------------------
SF.Net email is Sponsored by the Better Software Conference & EXPO
September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices
Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA
Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
