I wish to return to the question of Jmol and the display of H-bonds
in proteins which I let lapse after raising it a year or so back. I
would like Jmol to be able to display H-bonds between amino acid side
chains and main-chain atoms and have some questions for the
development team relevant to this.
Question 1: Jmol will display main-chain main-chain H-bonds in
proteins read from pdb files in which this information (or implied
info as secondary structure) does not appear to be present. Am I
right in thinking that Jmol calculates these, presumably while it is
calculating secondary structure?
Question 2: It was suggested to me that as I have the side-chain H-
bond info in a relational database (from the HBplus program) I could
add this to a pdb file, specifying CONECTS, and Jmol would interpret
this. However, it seems it would interpret this as covalent bonding
rather than H-bonding. What I want is to be able to turn this on and
off in the same way that I can script the current bonds. Anyone shed
some light on this?
Question 3: If the route suggested in 2 is not really an option, what
is the team's attitude to adding code to Jmol. A colleague has just
found some C code a student wrote many years ago that calculates side-
chain H-bonds. The advantage of this is that we have the source and
porting from C to Java would be less difficult than porting from some
other languages (e.g. Fortran). If I proposed it as a 15-week project
for a Masters student in Computing Science or IT, would this seem
feasible and would it be welcomed by the team?
David
___________________________________________________
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
http://motif.gla.ac.uk/
The University of Glasgow, charity number SC004401
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