Editing Advanced Coloring (section)

= See Also =
[[Color]], [[Spectrum]]

==Creating a Color bar==
To show a vertical/horizontal color bar indiacting the b-factor variation, use the script pseudobar.pml on the structure pseudobar.pdb, or do the following:
# Create a pdb-file which contains CA positions only, whereas the numbers correspond to your wanted increments of colors. Be sure that CA's are separated by a contant value, say 5 Angstroem.
# Load this new pseudobar-pdb file into PyMOL, make bonds between increment 1 and increment 2 [increment 2 and increment 3 and so on...], define/assign a smooth color for each increment (copy colors definition from automatically created colors made by b-factor script) and show the b-factor bar as lines (or sticks).

Also, see the newly created [[spectrumbar]] script!

==Coloring insides and outsides of helices differently==
The inside of helices can be adressed with:
<source lang="python">
set cartoon_highlight_color, red
</source>

 
==Coloring all objects differently==
Is there a simple way to colour each object currently loaded, with a different colour?
There is a script [[Color_Objects |color_obj.py]] that does the job.

USAGE

        color_obj(rainbow=0)

	This function colours each object currently in the PyMOL heirarchy
	with a different colour.  Colours used are either the 22 named
	colours used by PyMOL (in which case the 23rd object, if it exists,
	gets the same colour as the first), or are the colours of the rainbow

==List the color of atoms==
To retrieve the color for all residues in a selection, you can iterate over it from the PyMOL command line
<source lang="python">
iterate all, print color
</source>
In Python, it looks like this:
<source lang="python">
import pymol
pymol.color_list = []
cmd.iterate('all', 'pymol.color_list.append(color)')
print pymol.color_list
</source>

The colors listed will be in terms of Pymol indexing system, see [[Get Color Indices]] for converting to names or rgb values.

== See also ==
* [[Ramp_New]]


[[Category:Publication_Quality|Advanced Coloring]]
[[Category:Coloring|Advanced Coloring]]