On Mon, Jul 5, 2010 at 1:41 PM, Eric Martz <[email protected]>wrote:
> I was exploring item #15 set hbondsAngle/Distance at
> http://chemapps.stolaf.edu/jmol/docs/examples-11/new8.htm
>
> 1. It appears to me that "set hbondsAngleMinimum 120" has no effect
> on the subsequent calculate hbonds.
>
yes, I see that, too. OK, this is going to have to be a feature change. In
Jmol 11.8 there were just two ways to calculate hydrogen bonds -- the RasMol
way and a Jmol way. In both these cases these weren't really hydrogen bonds,
they were what I call "pseudo-hydrogen bonds" that do not involve actual H
atoms. When the value for hbondsAngleMinimum was 0, Jmol used the RasMol
calculation and ignored both the angle and distance checking; when it was
set to something else, Jmol used its own calculation and did the angle and
distance checking.
Jmol 12.0 introduces "true" hydrogen-bond calculation, and that changed the
picture. The change was that if you have a PDB file with no H atoms and you
do nothing special, Jmol will do just what it did before -- Rasmol hydrogen
bonds. But if you want Jmol's calculation of pseudoHydrogen bonds, rather
than obtusely setting the hbondsAngleMinimum value to something other than 0
degrees, you simply use
set hbondsRasmol false
Then hbondsAngleMinimum defaults to 90 and hbondsDistanceMaximum defaults to
3.25 for pseudo-hydrogen bonds and 2.5 for standard hydrogen bonds.
The choice of standard or pseudo simply revolves around whether hydrogen
atoms are in the selected atom set or not.
2. In order to help visualize such effects, I tried to show only the
> hbonds and no covalent bonds. (Later I realized all I had do say was
> "wireframe off", duh, but below is what I tried first.)
>
> Reload page to get a clean start.
>
> Click the first line under #15
>
> load 1crn.pdb;set hbondsAngleMinimum 90 # default
>
> then enter
>
> connect delete
>
> seems to work; you can still rotate and zoom. Now click the second line
>
> calculate hbonds {*} {*};color hbonds yellow;hbonds 0.1
>
Jmol freezes and is dead.
>
>
yeah, don't do that. You just wrecked all the polymer structures, and Jmol
needs the N atom connections so that it can calculate the Rasmol hbond
energies. But I've fixed that bug anyway.
> -Eric
>
>
>
>
>
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--
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
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