David -- none of the work I just did will be of help to you, since you have
the H atoms already present. But I'm glad you started this discussion
anyway, because that will certainly be of interest to others.
I really think a simple command such as
connect 1.8 {H and connected(_O or _N)} {_O or _N} HBONDS CREATE
is all you need.
Bob
On Tue, Nov 4, 2008 at 6:06 PM, David Leader <[EMAIL PROTECTED]> wrote:
> 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.
>
>
> 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
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
