Difference between revisions of "Color"
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* [[Advanced Coloring]]
* [[Advanced Coloring]]
Revision as of 17:13, 2 March 2016
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.
- 1 USAGE
- 2 PYMOL API
- 3 EXAMPLES
- 4 SEE ALSO
color color-name color color-name, object-name color color-name, (selection)
cmd.color( string color, string selection )
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
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,
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
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 resi = split[1:-1] phi_ppm2 = float(split) phi_ppm2_err = float(split) R2_0 = float(split) R2_0_err = float(split) 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)
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:
# 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) # use cmd.get_color_tuple(color) to convert color index to RGB values print stored.list
Or, you can label each atom by it's color code:
label all, color
What colors does PyMOL currently have?
basic colors can be manually accessed and edited from the PyMOL menu under Setting --> Colors...
At the Pymol prompt, you can use the command Get Color Indices to get a list of Pymols named colors.
Get_colors is a script that allows accessing colors as well.
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")