Editing Color (section)

== Examples ==

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

=== Color by element, except carbons ===

 color atomic, (not elem C)

=== Use a custom RGB color ===

 color 0x006600

===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, palette, object_name
</source>

For available palettes and more details see: [[spectrum]]

===B-Factors===
The command to color a molecule by B-Factors (B Factors) is:
<source lang="python">
spectrum b, selection=SEL
</source>
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.
<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.

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/)

====Reassigning B-Factors and Coloring - from file ====
<source lang="python">
reinitialize
prot="1XYZ"
cmd.fetch(prot,async=0)

# Set b value to zero
cmd.alter(prot,b=0.0)
cmd.show_as("cartoon",prot)

python
inFile = open("phi_values.txt", 'r')
val_list = []
for line in inFile.readlines()[1:]:
    split = line.split()
    resn = split[0][0] 
    resi = split[0][1:-1]
    phi_ppm2 = float(split[1])
    phi_ppm2_err = float(split[3])
    R2_0 = float(split[4])
    R2_0_err = float(split[6])
    print "Resn=%s Resi=%s, phi_ppm2=%2.2f, phi_ppm2_err=%2.2f, R2_0=%2.2f, R2_0_err=%2.2f"%(resn,resi,phi_ppm2,phi_ppm2_err,R2_0,R2_0_err)

    val_list.append(phi_ppm2)
    cmd.alter("%s and resi %s and n. CA"%(prot,resi), "b=%s"%phi_ppm2)

python end
minval = min(val_list)
print minval
maxval = max(val_list)
print maxval
cmd.spectrum("b", "blue_white_red", "%s and n. CA"%prot, minimum=0, maximum=maxval)
cmd.ramp_new("ramp_obj", prot, range=[0, minval, maxval], color="[blue, white, red ]")
cmd.save("%s_newBFactors.pdb"%prot, "%s"%prot)
</source>

=== 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:
<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.

=== Getting Atom Colors ===
<source lang="python">
stored.list = []
iterate all, stored.list.append(color) # use cmd.get_color_tuple(color) to convert color index to RGB values
print stored.list
</source>

Or, you can [[label]] each atom by it's color code:
<source lang="python">
label all, color
</source>

=== What colors does PyMOL currently have? ===
basic colors can be manually accessed and edited from the PyMOL menu under '''Setting''' --> '''Colors...'''<br>
At the Pymol prompt, you can use the command [[Get Color Indices]] to get a list of Pymols named colors.<br>
[[Get_colors]] is a script that allows accessing colors as well.<br>

=== Color States Individually ===
<source lang="python">
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)
</source>
Or, we can do it differently,
<source lang="python">
# 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")
</source>