Difference between revisions of "Color"
(Expanded some examples included the new B Factor coloring mini-script.) |
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Line 18: | Line 18: | ||
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> | ||
+ | |||
+ | ===B-Factors=== | ||
+ | The command to color your molecule by B-Factors (B Factors) is: | ||
+ | <source lang="python"> | ||
+ | cmd.spectrum("b", selection="SEL"); | ||
+ | </source> | ||
+ | where '''SEL''' is your 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> | ||
+ | |||
+ | |||
[[Category:Objects_and_Selections]] | [[Category:Objects_and_Selections]] | ||
[[Category:Commands|color]] | [[Category:Commands|color]] |
Revision as of 11:53, 15 February 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
B-Factors
The command to color your molecule by B-Factors (B Factors) is:
cmd.spectrum("b", selection="SEL");
where SEL is your 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")