Pat,
Here's my initial solution, ready for testing in 11.5.12. It's a
compromise between not changing Jmol enough to cause problems with
compatibility and wanting to make it possible to have better control
over Van der Waals radii. It involves several new capabilities:
--Three internal lists: Jmol, Babel, and Rasmol. Any one of these three
lists can be designated as the one for defining default vdw radii. These
settings persist through file loading, like element colors. (They do not
get reset with ZAP.)
set defaultVDW Jmol
set defaultVDW Babel
set defaultVDW Rasmol
--Users can also load their own list or modify these lists with selected
values using the DATA command. The basis is always whatever list is
currently set, then
DATA "element_vdw"
the following is user-defined data
note that only numeric data are parsed
so all these lines are ignored
just don't put any numbers here!
1 1.0 //H
6 1.7 //C
7 1.6 //N
END "element_vdw"
set defaultVDW User
or, more compactly, with semicolons:
DATA "element_vdw" 1 1.0; 6 1.7; 7 1.6 END "element_vdw"
set defaultVDW User
--You can show these using
show vdw # the current defaults
show vdw Jmol
show vdw Babel
show vdw Rasmol
show vdw User
--Saving the state also saves user vdw information; you can check that
to see just the specific values you have changed.
--You can show individual atom vdw settings using LABEL %V
--You can also directly set the vdw radius of any selected atom(s) to
anything you want. This information is also saved in the state and can
be displayed using "show state"
{carbon}.vdw = 1.7
{atomno=2}.vdw = 1.8
--Note that {carbon}.vdw=1.7 is NOT persistent, because that just says,
"select all the carbons and set their radius to 1.7", not "set elemental
carbon vdw to always be 1.7" -- to do that you must use the DATA statement:
DATA "element_vdw" 6 1.7 END "element_vdw"
--If you do change values, you must do a SPACEFILL command again to
incorporate these changes in the actual displayed model. In general, it
is recommended that element-based settings be done prior to file loading.
--The SPACEFILL, HALO and STAR commands now all have the same format.
(They mostly did before, but this is better.) This format includes a way
of indicating percentage of the vdw radius based on any of the four lists.
star 100%Babel
halo 50%Jmol
spacefill 40% # of the current settings or specified atom radius
stars 1.7 # 1.7 anstroms
spacefill +1.2 # 1.2 angstroms larger than the current vdw defaults or
specific atom settings
stars @x%Babel # math is fully implemented (make sure x is an integer)
stars @{x + 10}%Jmol # x must be an integer
--Initial program defaults for file loading display atoms as spacefill
20%Jmol, as before. This is independent of what is the current
defaultVDW setting. Initial zoom is based on the Jmol vdw list, again,
regardless of the settings.
--The DOTS, GEOSURFACE, and ISOSURFACE commands use whatever is the
current default setting or whatever specific atom settings have been made.
Seems to me that should be enough to at least get us started. Pat, it's
amazing how bloated the Jmol setting for spacefill looks when you can
switch back and forth. Hmm. Sure appreciate your pointing that out.
Bob
Patrick J. Carroll wrote:
>I remember a discussion a couple years ago about the van der Waal's radii used
>in Jmol. There was a feeling that the values in Jmol are somewhat
>"over-estimated". Is there a way that a user can input his own radii? (other
>than using the explcit "spacefill 1.70" every time he wants to draw a van der
>Waals carbon atom). Or, alternatively, can the values in JmolConstants.jave be
>changed to those in, e.g., A. Bondi, J. Phys. Chem, vol.68, p.441 (1964) -
>which, I think, are widely accepted.
>
>
>Pat Carroll
>U of Penn
>Phila, PA
>
>
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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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