On Wed, Jul 7, 2010 at 3:59 PM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> Thanks for fixing the bugs I reported in the past couple of days! And
> thanks for adding "set hbondsrasmol true|false". I confirm that in
> new8.htm the examples #15 and #53 now seem to work as expected.
>
>
great
> Re "color hbonds energy": It is not obvious to me whether blue is
> high (weak) or low (strong) energy. Please state this under
> #colorbondobject.
>
>
red is "hot" -- high energy; blue is "cold" -- low energy, like temperature.
I've added it to the documentation on hydrogen bonds. I'll try to remember
to add it there in color bond as wells.
> Is there a way to report the hbond energy values for pairs of hbonded
> atoms? Could it be reported by hover? Or could it be reported as a
> number attached to the bond, similarly to distance monitors? I'm not
> necessarily asking for these features, just curious how one could
> find out the energy values.
>
>
I hesitate to give values for "energy" when it is such an ad-hoc very crude
value. It's just a
crude guide -- like the color -- to what we are seeing there. A way of
making some sort of
distinction among hydrogen bonds.
If you want to take a look at the values, check the state. They are listed
there now in the data table for those bonds.
> I am unclear which of the three "calculate hbonds" methods uses DSSP.
> Could you please clarify that in the documentation at #calculate?
>
>
Sure. I can do that. The DSSP calculation is used whenever you have
setHbondsRasmol TRUE and there are no H atoms selected.
> Does DSSP use hbondsAngleMinimum? I think not because I think that
> the RasMol-hbonds calculation uses DSSP and the Jmol-hbonds
> calculation does not.
>
>
no, it just uses this calculation:
http://en.wikipedia.org/wiki/DSSP_%28protein%29
> I cannot understand what the RasMol-hbonds TYPE colors represent in
> "color hbonds TYPE". Under calculate in the documentation, there is a
> link from "color hbonds TYPE" to #colorbondobject but there is no
> mention of TYPE under hbonds there. Or of the energy color scheme.
>
>
Isn't that on the Wiki? Maybe I lost the link there. "type" means now many
residues away it is for DSSP.
http://jmol.sourceforge.net/jscolors/#Hydrogen%20bonds
> Thanks, -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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