Hmm. Interesting. That's a bug.
On Sun, Jun 17, 2012 at 10:41 AM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> In Jmol 11.8, ssbonds inherited the color of cys.sg atoms, even when
> "set ssbonds backbone".
> Thus, in FirstGlance in Jmol, I could color the backbone-connecting
> ssbonds by coloring the cys.sg:
>
> select all
> ssbonds 1.0
> select cys.sg
> color ssbonds none
> color [xffff30] # or "color chain"
> set ssbonds backbone
>
> However in Jmol 12, the ssbonds inherit the cys.sg color only when
> "set ssbonds sidechain", not when "set ssbonds backbone". In Jmol 12,
> backbone-ssbonds inherit the color of cys.ca.
>
> Was this change intentional? I can change the code in FirstGlance but
> before doing that I wanted find out if the change was unintentional
> and hence will be changed back to the old behavior.
>
> Personally I prefer the old behavior: since ssbonds represent bonds
> between cys.sg, I think it makes sense for them to inherit the color
> of cys.sg even when they are represented as connecting backbones.
>
> Thanks, -Eric
>
>
>
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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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