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Difference between revisions of "Color"
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List of [[Color Values]] | List of [[Color Values]] | ||
| − | === | + | ==EXAMPLES== |
| + | ===Color all carbons yellow=== | ||
<source lang="python">color yellow, (name C*)</source> | <source lang="python">color yellow, (name C*)</source> | ||
| − | RGB Example | + | ===RGB Example=== |
<source lang="python"> | <source lang="python"> | ||
set_color khaki, [195,176,145] | set_color khaki, [195,176,145] | ||
color khaki | color khaki | ||
</source> | </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. | ||
| + | |||
| + | ====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. | ||
| + | |||
[[Category:Objects_and_Selections]] | [[Category:Objects_and_Selections]] | ||
[[Category:Commands|color]] | [[Category:Commands|color]] | ||
Revision as of 14:54, 22 March 2007
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
cmd.color( string color, string selection )
Using RGB for Color
If you prefer RGB to color any object
set_color newcolor, [r,g,b]
color newcolor
List of Color Values
EXAMPLES
Color all carbons yellow
color yellow, (name C*)
RGB Example
set_color khaki, [195,176,145]
color khaki
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, x, object_name
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:
cmd.spectrum("b", selection="SEL");
where SEL is a valid selection, for example, "protA and n. CA", for protein A's alpha carbons.
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.