Color

2008-05-20T15:53:39Z

Domsicj: reversed order of "ramp_obj" and "your-objec-name" for the "set surface_color" option.

===DESCRIPTION===
'''color''' changes the color of an object or an atom selection.

===USAGE===
color color-name
color color-name, object-name
color color-name, (selection)

===PYMOL API===
<source lang="python">cmd.color( string color, string selection )</source>

==Using RGB for Color==
If you prefer RGB to color any object
<source lang="python">
set_color newcolor, [r,g,b]
color newcolor
</source>
List of [[Color Values]]

==EXAMPLES==
===Color all carbons yellow===
<source lang="python">color yellow, (name C*)</source>

===RGB Example===
<source lang="python">
set_color khaki, [195,176,145]
color khaki
</source>

===Color by Spectrum Example===
Color by spectrum is in the GUI menu but did you realize that the spectrum is not limited to a simple rainbow?
<source lang="python">
spectrum count, x, object_name
</source>
x can can be anyone of the following:
blue_green, green_white_magenta, red_cyan, blue_magenta, green_white_red, red_green, blue_red, green_white_yellow, red_white_blue, blue_white_green, green_yellow, red_white_cyan, blue_white_magenta, green_yellow_red, red_white_green, blue_white_red, magenta_blue, red_white_yellow, blue_white_yellow, magenta_cyan, red_yellow, blue_yellow, magenta_green, red_yellow_green, cbmr, magenta_white_blue, rmbc, cyan_magenta, magenta_white_cyan, yellow_blue, cyan_red, magenta_white_green, yellow_cyan, cyan_white_magenta, magenta_white_yellow, yellow_cyan_white, cyan_white_red, magenta_yellow, yellow_green, cyan_white_yellow, rainbow, yellow_magenta, cyan_yellow, rainbow2, yellow_red, gcbmry, rainbow2_rev, yellow_white_blue, green_blue, rainbow_cycle, yellow_white_green, green_magenta, rainbow_cycle_rev, yellow_white_magenta, green_red, rainbow_rev, yellow_white_red, green_white_blue, red_blue, yrmbcg

===B-Factors===
The command to color a molecule by B-Factors (B Factors) is:
<source lang="python">
cmd.spectrum("b", selection="SEL");
</source>
where '''SEL''' is a valid selection, for example, "protA and n. CA", for protein A's alpha carbons.

You can choose the spectrum you want with the command:
<source lang="python">
cmd.spectrum("b", 'rainbow', selection="SEL");
</source>

where '''rainbow''' is a valid selection from the list:
<pre>
blue_green green_white_magenta red_cyan
blue_magenta green_white_red red_green
blue_red green_white_yellow red_white_blue
blue_white_green green_yellow red_white_cyan
blue_white_magenta green_yellow_red red_white_green
blue_white_red magenta_blue red_white_yellow
blue_white_yellow magenta_cyan red_yellow
blue_yellow magenta_green red_yellow_green
cbmr magenta_white_blue rmbc
cyan_magenta magenta_white_cyan yellow_blue
cyan_red magenta_white_green yellow_cyan
cyan_white_magenta magenta_white_yellow yellow_cyan_white
cyan_white_red magenta_yellow yellow_green
cyan_white_yellow rainbow yellow_magenta
cyan_yellow rainbow2 yellow_red
gcbmry rainbow2_rev yellow_white_blue
green_blue rainbow_cycle yellow_white_green
green_magenta rainbow_cycle_rev yellow_white_magenta
green_red rainbow_rev yellow_white_red
green_white_blue red_blue yrmbcg
</pre>

====Reassigning B-Factors and Coloring====
It is commonplace to replace the B-Factor column of a protein with some other biochemical property at that residue, observed from some calculation or experiment. PyMOL can easily reassign the B-Factors and color them, too. The following example will load a protein, set ALL it's B Factors to "0", read in a list of properties for each alpha carbon in the proteins, assign those new values as the B-Factor values and color by the new values. This example is possible because commands PyMOL does not recognize are passed to the Python interpreter --- a very powerful tool.
<source lang="python">
# load the protein
cmd.load("protA.pdb")

# open the file of new values (just 1 column of numbers, one for each alpha carbon)
inFile = open("newBFactors", 'r')

# create the global, stored array
stored.newB = []

# read the new B factors from file
for line in inFile.readlines(): stored.newB.append( float(line) )

# close the input file
inFile.close()

# clear out the old B Factors
alter protA, b=0.0

# update the B Factors with new properties
alter protA and n. CA, b=stored.newB.pop(0)

# color the protein based on the new B Factors of the alpha carbons
cmd.spectrum("b", "protA and n. CA")
</source>

If you want to save the file with the new B Factor values for each alpha carbon,
<source lang="python">
cmd.save("protA_newBFactors.pdb", "protA")
</source>
or similar is all you need.

===== Expanding to Surface =====
If you have run the above code and would like the colors to be shown in the [[Surface]] representation, too, then you need to do the following:
<source lang="python">
# Assumes alpha carbons colored from above.
create ca_obj, your-object-name and name ca
ramp_new ramp_obj, ca_obj, [0, 10], [-1, -1, 0]
set surface_color, ramp_obj, your-object-name
</source>

Thanks to Warren, for this one.

[[Category:Objects_and_Selections]]
[[Category:Commands|color]]

PyMOL Wiki - User contributions [en]

Color