On Fri, Feb 22, 2013 at 5:23 PM, Spencer Bliven <sbli...@ucsd.edu> wrote:
> I've been trying to customized some jmol scripts and I had a couple
> questions.
>
> 1. Is there an option to change the length of the arrowhead for a
> 'draw arrow' or 'draw arrow arc' command?
>
>
size overall, but not length per se.
set defaultDrawArrowScale (decimal)
*Sets the default scale for the arrow tip for
arrows.<http://chemapps.stolaf.edu/jmol/docs/?ver=13.0#draw>
*
>
> 1. What are the units for the 'scale' parameter for an arc? I've found
> that a value of 500 results in an arc about 1A in radius for my test
> protein, but I assume this is somehow proportionate to the input points.
>
>
*The SCALE parameter is used to set the diameter of the overall circle
containing the arc. *
draw scale 2.0 arc.... 2-Angstrom diameter
draw scale 500 arc ... 5-Angstrom diameter
> 1. What's the best way to draw a line without an arrow head? Use 'draw
> cylinder'?
>
> Yes, I think so.
> I'm running Jmol 12.0.22 through BioJava.
>
We need to get BioJava gurus to move to Jmol 13. (Andreas? Peter?) Maybe
there is a newer version of BioJava than what you are using.
> I have to say that the
> documentation<http://chemapps.stolaf.edu/jmol/docs/#draw>for the draw command
> is rather confusing, since some of the "modifying
> options" are mutually exclusive or change meanings depending on other
> options.
>
Probably in need of an upgrade.
> Thanks,
>
> Spencer Bliven
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
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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