right, that's a, ah FEATURE. Right now the code reads:
boolean addHbonds = viewer.hbondsAreVisible();
setShapeProperty(JmolConstants.SHAPE_STICKS, "type", new Integer(
JmolConstants.BOND_HYDROGEN_MASK));
viewer.setShapeSize(JmolConstants.SHAPE_STICKS, 0, bsConfigurations);
if (addHbonds)
viewer.autoHbond(bsConfigurations, bsConfigurations, null);
viewer.select(bsConfigurations, tQuiet);
This is there to recreate the hydrogen bonds if they have been
calculated for one conformation, and then another is displayed. The
first part turns them off for the atoms involved in the conformation;
the second part turns them on again. It's not ideal.
The solution is to use
connect (159.O%A) (162.H%A) partial 1.1
This makes a bond that Looks like a hydrogen bond, but is really a partial
bond.
Bob
Angel Herraez wrote:
>I have a PDB model of a beta turn (attached). With "hbonds calculate", Jmol
>finds the
>expected Hbond and draws it between O and N. I want to have instead an H bond
>going
>from O to H, so I decided not to calculate Hbonds and to define my own using
>"connect".
>
>However, I am finding that Jmol is adding and showing the calculated-would-be
>bond too,
>and even removing the given one. This only happens on my model when it has 2
>alternative
>configurations.
>
>1. Load the model
>2. Change between the 2 alternates, using pop-up menu -- everything OK
>3. Now do "connect (159.O%A) (162.H%A) hbond"
>4. Repeat step 2 and see how the non-intended Hbond shows up and the defined
>one even
>dissapears
>
>Tested on 11.2.14 and 11.3.41
>
>Thanks for any clues
>
>
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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