On Sep 14, 2005, at 3:12 , Jan wrote:
Bob Hanson wrote:
color atoms CPK
returns the selected atoms to their "default" color, which may no
longer really be CPK colors. For example:
color atoms chain
color carbon green
color atoms CPK
returns the selected atoms to their "default" color, which for
carbon has now been defined as green.
Because there are only a limited number of schemes this is an
indispensable feature to manipulate the "default" color set.
But I agree, that this may be confusing.
There are other color manipulations which 'will have to wait' but
would be helpful e.g.
color label amino
(besides the fact, that the amino color scheme should be open to
manipulations as the atom color scheme or any other scheme)
this is an interesting issue. on the one hand, it is useful to be
able to change the underlying colors of a scheme, especially if you
want consistency between different display elements (i.e., to match a
Jmol figures with a textbook figure).
OTOH, one could argue that a color scheme is more powerful if it
remains consistent within itself - in other words, alpha helices
always red, beta strands yellow, turns blue, etc. (this was one
motive for establishing the DRuMS set of schemes, btw.)
to use Bob's example, to me, CPK has a certain set of colors
associated with it (with carbon as black or dark gray). so if I saw
a green sphere in a molecule, I would not immediately associate it
with carbon (chlorine is more like it). if I saw a lot of green
spheres in an obvious protein context, I could certainly reach the
logical conclusion that it is probably not chlorine - but the
associative link between color and element identity would not be as
strong now.
for my own purposes, I tend to support keeping schemes consistent
within themselves, to maximize the power of color as a tool for
communicating information. but, that said, I am pretty sure that
this should be a pedagogical decision, and *not* decided at the
software level.
NONE is not DEFAULT, it means hereted from ancestor element (in
most cases, this would be the actual atom color). NONE is
indispensable. NONE is part of the RasMolScripting language.
Regards, Jan
I agree; NONE is indispensable. I think it is not quite so
straightforward to determine what should be the 'actual atom color'
though. in Rasmol, I think it defaults to the Rasmol CPK scheme (?)
- but I think it is more complicated in Jmol.
tim
--
Timothy Driscoll
molvisions - see. grasp. learn.
<http://www.molvisions.com/>
earth:usa:virginia:blacksburg
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