Timothy Driscoll wrote:
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.)
This is your private scheme, not suported by me. You may try to use Jmol
to promote it, but I like the freedom to continue using an alternative
one, other programs color stands blue by default (but this could be
altered of corse) e.g. MolMol standard ribbon.mac
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
you are right CPK is a color scheme but the scripting language misuse it
to "reset to current scheme" whatever the scheme is
rasmol
jmol
drums
molmol
setor
jil
or altered by
select <element> color
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.
Our carbon source are green plants, if you need a hint ;-) and more
important the contrast of green is much better
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.
I agree, software should be open.
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.
This is the color, which is associated with the atom at any moment,
coloring e.g. a label with NONE would make it "transparent" so it takes
the color of the atom as the label color
in Rasmol, I think it defaults to the Rasmol CPK scheme (?) - but I
think it is more complicated in Jmol.
if you do
color carbon green
color cartoon none
# in RasMol (and Jmol) the *.CA transmit the green atom color to color
cartoon
select *.CA
color atom gray
# the carton color switched to gray (in RasMol and Jmol)
# note that there could be a difference
select carbon
color atom green
# and in contrast
color carbon green
#
color carbon <color>
# should manipulate the scheme while
color atom <color>
# should manipulate only "atom color" property of the selection.
color cartoon cpk
# use the active (modified) scheme color for carbon
color cartoon none
# use the atom color of the *.CA at any moment
# try:
load pdb 1plc.pdb
cartoon
color carbon green
select *.CA and (1-15)
color atom yellow
select *.CA and (26-33,74-66)
color atom cyan
select all
color cartoon cpk
color cartoon none
select *.CA and (15-26)
color atom pink
select all
color cartoon cpk
select *.CA and (55-66)
color atom gray
Regards, Jan
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