Post by s datI think this is what happened. I was using the preset publication command to
to change settings after you apply one of these. These are somewhat
are nearly impossible to recover.
Actually, I fell into this trap a few years ago. Warren would just
used these commands.
Post by s datHi Tsjerk
Now it DOES change the color of the inside of helixes. Thank you so much.
I think this is what happened. I was using the preset publication command to
generate cartoons and then changing things. Once preset publication is
invoked the command set cartoon_highlight_color, blue does not change
anything. When I tried to use what you suggested on the same file (set
cartoon_highlight_color, blue, helix A) it changed the color for the whole
molecule, not just helix A.
So I started with a fresh pdb file and now it seems that by default pymol
colors the inside and outside of the helix the same. And when I make
selections and change colors for that selection, the changes including the
colors of the inside of the helix are confined to that selection.
Thank you again, it was driving me nuts.
sdat5885
Post by Tsjerk WassenaarHi Sdat5885,
Have you started a fresh session, or did you a. load a session file or
b. did some other things you didn't mention before? It may be that you
have specifically set the highlight color for your protein. The
default is not grey, but whatever color the C alpha atom has. You
set cartoon_highlight_color, blue, object_to_highlight
Cheers,
Tsjerk
Post by s datHi Jason
Sorry but it does not work. The version is PyMOL 0.99rc6, OS is XP
Professional 2002 SP3.
Thanks for the help,
Sdat5885
On Sun, Aug 15, 2010 at 6:44 PM, Jason Vertrees
Post by Jason VertreesVitaly is right,
"set cartoon_highlight_color, blue"
will set the inside helical color to blue. If you're having problems,
please let us know which version of PyMOL you're using and on which OS
(including version).
Cheers,
-- Jason
Post by s datDear All
set cartoon_highlight_color, blue does not change anything in my figure.
If
Setting: cartoon_highlight_color set to default.
The default right now is grey. I tried to go into settings, change the
default to for ex blue, and then tried to recolor but nothing happened !
Thanks
sdat5885
Post by Vitaly VostrikovHello,
set cartoon_highlight_color, blue
Vitaly
----- Original Message -----
Date: Saturday, August 14, 2010 11:08 pm
Subject: [PyMOL] Newbie question : what command to use for changing color
of inside of helix
Post by s datDear All
The default setting for color of inside of helices is grey. I am
trying to
color helices the same, both inside and outside. I tried using
cartoon_highlight_color, blue but that does not change the grey to
blue. Any
help would be greatly appreciated.
Thanks
sdat5885
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