Color: Difference between revisions
(arguments) |
|||
(17 intermediate revisions by 8 users not shown) | |||
Line 1: | Line 1: | ||
'''color''' sets the color of an object or an atom selection to a predefined, named color, an RGB hex color, or a color [[ramp_new|ramp]]. | |||
'''color''' | For an overview of predefined 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 == | |||
<source lang="python"> | <source lang="python"> | ||
color color-name | color color-name | ||
Line 8: | Line 12: | ||
</source> | </source> | ||
== | == Arguments == | ||
* color-name = str or int: [[Color Values|named color]], index of a named color, <code>0xRRGGBB</code> string, <code>0x40RRGGBB</code> integer, name of a [[ramp_new|ramp]] object, or special value <code>atomic</code> | |||
* object-name = str: Name of an object or name pattern (with Asterisk (<code>*</code>)) which matches multiple objects. Changes the [[set_object_color|object color]], and if it is a molecular object, also the color of all atoms. {default: all} | |||
* selection = str: [[Selection Algebra|atom selection]], this is any expression which is not a valid object pattern. E.g. an expression which starts with a parentheses. This will only color atoms, not objects. | |||
== | == Examples == | ||
===Color all carbons yellow=== | ===Color all carbons yellow=== | ||
<source lang="python">color yellow, (name C*)</source> | <source lang="python">color yellow, (name C*)</source> | ||
=== | === Color by element, except carbons === | ||
color atomic, (not elem C) | |||
color | |||
=== Use a custom RGB color === | |||
color 0x006600 | |||
===Color by Spectrum Example=== | ===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? | 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"> | <source lang="python"> | ||
spectrum count, | spectrum count, palette, object_name | ||
</source> | </source> | ||
For available palettes and more details see: [[spectrum]] | |||
===B-Factors=== | ===B-Factors=== | ||
The command to color a molecule by B-Factors (B Factors) is: | The command to color a molecule by B-Factors (B Factors) is: | ||
<source lang="python"> | <source lang="python"> | ||
spectrum b, selection=SEL | |||
</source> | </source> | ||
where '''SEL''' is a valid selection, for example, "protA and n. CA", for protein A's alpha carbons. | 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==== | ====Reassigning B-Factors and Coloring==== | ||
Line 108: | Line 83: | ||
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/) | 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 === | === 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: | 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"> | <source lang="python"> | ||
Line 123: | Line 136: | ||
<source lang="python"> | <source lang="python"> | ||
stored.list = [] | stored.list = [] | ||
iterate all, stored.list.append(color) | iterate all, stored.list.append(color) # use cmd.get_color_tuple(color) to convert color index to RGB values | ||
print stored.list | print stored.list | ||
</source> | </source> | ||
Line 132: | Line 145: | ||
</source> | </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 === | === Color States Individually === | ||
Line 160: | Line 177: | ||
</source> | </source> | ||
[[Category:Objects_and_Selections]] | == See Also == | ||
[[Category:Commands| | |||
* [[Advanced Coloring]] | |||
* [[Get Color Indices]] | |||
* [[spectrum]] | |||
* [[Ramp_New]] | |||
[[Category:Objects_and_Selections|Color]] | |||
[[Category:Commands|Color]] | |||
[[Category:States|Coloring states individually]] | [[Category:States|Coloring states individually]] | ||
[[Category:Coloring|Color]] |
Latest revision as of 11:21, 24 October 2019
color sets the color of an object or an atom selection to a predefined, named color, an RGB hex color, or a color ramp. For an overview of predefined 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)
Arguments
- color-name = str or int: named color, index of a named color,
0xRRGGBB
string,0x40RRGGBB
integer, name of a ramp object, or special valueatomic
- object-name = str: Name of an object or name pattern (with Asterisk (
*
)) which matches multiple objects. Changes the object color, and if it is a molecular object, also the color of all atoms. {default: all} - selection = str: atom selection, this is any expression which is not a valid object pattern. E.g. an expression which starts with a parentheses. This will only color atoms, not objects.
Examples
Color all carbons yellow
color yellow, (name C*)
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?
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/)
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[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)
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) # 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")