Angel wrote:
> David, have you measured the length of the Hbonds you want to show up?
> You might nedd some longer spec.
> I've just tested
> connect 1.8 {_H and connected(_O or _N)} {_O or _N} HBONDS CREATE;
> with
> http://doolittle.ibls.gla.ac.uk/top500H/1osaH.pdb
> and Jmol 11.6.3 and it creates and draws 12 new Hbonds
Thanks Angel. I've tried that, but the 12 don't include the important
ones for me.
The point is that these are Hbond identified on the basis of energy
using the HBplus program, not just distance, and deposited in my
database. The motifs I visualize are identified by angle criteria
together with the existance of these HBonds, again from my database.
Bob wrote:
> connect 2.5 {_H and connected(_O or _N)} {(_O or _N) and not within
> (group,
> _1)} HBONDS CREATE
OK, that probably includes the ones I want (difficult to see because
the hydrogens are not there) but the number of background hydrogen
bonds make it look awful.
Sorry to have wasted your time, but I'm now convinced that the SQL
route is the way I'm going to have to go. I've tested a query that
finds the Hbonds associated with the atoms in a three-residue motif
which takes 4 secs to run (wasn't so difficult to formulate after all
- only involved three tables). There are about 8 hbonds in the
resulting table, two of which have the same id, and I can draw using
their atom numbers (which are retrieved). If I can do some DB
indexing to reduce the query time by an order of magnitude I think
I'll be able to produce what I want with another query on the
resulting table.
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
The University of Glasgow, charity number SC004401
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