Color

color sets the color of an object or an atom selection to a predefined, named color. For an overview of predifined colors, see Color Values. For a script that enumerates all the colors see, List_Colors. If you want to define your own colors, see Set_Color.

USAGE

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

PYMOL API

cmd.color( string color, string selection )

EXAMPLES

Color all carbons yellow

color yellow, (name C*)

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?

spectrum count, palette, object_name

For available palettes and more details see: spectrum

B-Factors

The command to color a molecule by B-Factors (B Factors) is:

spectrum b, selection=SEL

where SEL is a valid selection, for example, "protA and n. CA", for protein A's alpha carbons.

For more details see: spectrum

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.

# 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")

If you want to save the file with the new B Factor values for each alpha carbon,

cmd.save("protA_newBFactors.pdb", "protA")

or similar is all you need.

A script (data2bfactor.py) that loads data into the B-factor (b) or occupancy (q) columns from an external file can be found in Robert Campbell's PyMOL script repository (http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/)

Expanding to Surface

See Expand_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:

# 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

Thanks to Warren, for this one.

Getting Atom Colors

stored.list = []
iterate all, stored.list.append(color)
print stored.list

Or, you can label each atom by it's color code:

label all, color

Color States Individually

fetch 1nmr
set all_states

# the object has 20 states, so we can set separate line colors
# for each state as follows:
for a in range(1,21): cmd.set("line_color","auto","1nmr",a)

Or, we can do it differently,

# start over,
fetch 1nmr

# break apart the object by state
split_states 1nmr

# delete the original
dele 1nmr

# and color by object (carbons only)
util.color_objs("elem c")

# (all atoms)
util.color_objs("all")

SEE ALSO

• Advanced Coloring
• spectrum