Spectrum: Difference between revisions
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[[Image:Spectrum_ex2.png|right|thumb|185px]] | [[Image:Spectrum_ex2.png|right|thumb|185px]] | ||
[[Spectrum]] colors atoms with a spectrum of colors based on an atomic property. | [[Spectrum]] colors atoms with a spectrum of colors based on an atomic property. | ||
''New in PyMOL 1.6: Supports any [[iterate]] expression, like [[spectrumany]]'' | |||
''New in PyMOL 1.6: Supports space separated color list as palette, like [[spectrumany]]'' | |||
= Usage = | = Usage = | ||
<source lang="python"> | <source lang="python"> | ||
| Line 9: | Line 12: | ||
''expression'' | ''expression'' | ||
::count | ::count (atom count), pc (partial charge), or any expression which is valid for [[iterate]]. Non-numerical values will be enumerated (e.g. chain) {default: count} | ||
''palette'' | ''palette'' | ||
::string: palette name {default: rainbow} | ::string: palette name, or space separated list of colors {default: rainbow} | ||
''selection'' | ''selection'' | ||
| Line 27: | Line 30: | ||
= Notes = | = Notes = | ||
Minimum and maximum are determined automatically unless '''both''' arguments are provided and ''minimum < maximum''. | |||
Available palettes include: | Available palettes include: | ||
*blue_green | *blue_green | ||
| Line 66: | Line 71: | ||
*rainbow_cycle | *rainbow_cycle | ||
*rainbow_cycle_rev | *rainbow_cycle_rev | ||
*rainbow_rev red_blue | *rainbow_rev | ||
*red_cyan red_green | *red_blue | ||
*red_cyan | |||
*red_green | |||
*red_white_blue | *red_white_blue | ||
*red_white_cyan | *red_white_cyan | ||
| Line 94: | Line 101: | ||
spectrum count, rainbow_rev, chain A, byres=1 | spectrum count, rainbow_rev, chain A, byres=1 | ||
</source> | </source> | ||
Non-numerical property (Since PyMOL 1.6): | |||
spectrum chain | |||
Custom color list (Since PyMOL 1.6): | |||
spectrum b, blue yellow cyan neon pink grey | |||
== Intermediate == | == Intermediate == | ||
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* [[Advanced Coloring]] | * [[Advanced Coloring]] | ||
* [[Palette Colorbars]] | |||
* [[Advanced_Coloring#Coloring_with_.27chainbows.27_from_a_script|chainbow]] | * [[Advanced_Coloring#Coloring_with_.27chainbows.27_from_a_script|chainbow]] | ||
* [[spectrumany]] | * [[spectrumany]] | ||
* [[Ramp_New]] | |||
* [[spectrumbar]] | |||
Latest revision as of 13:56, 22 October 2019
Spectrum colors atoms with a spectrum of colors based on an atomic property.
New in PyMOL 1.6: Supports any iterate expression, like spectrumany
New in PyMOL 1.6: Supports space separated color list as palette, like spectrumany
Usage
spectrum [expression [, palette [, selection [, minimum [, maximum [, byres ]]]]]]
expression
- count (atom count), pc (partial charge), or any expression which is valid for iterate. Non-numerical values will be enumerated (e.g. chain) {default: count}
palette
- string: palette name, or space separated list of colors {default: rainbow}
selection
- string: atoms to color {default: (all)}
minimum
- float: {default: None (automatic)}
maximum
- float: {default: None (automatic)}
byres
- integer: controls whether coloring is applied per-residue {default: 0}
Notes
Minimum and maximum are determined automatically unless both arguments are provided and minimum < maximum.
Available palettes include:
- blue_green
- blue_magenta
- blue_red
- blue_white_green
- blue_white_magenta
- blue_white_red
- blue_white_yellow
- blue_yellow
- cbmr
- cyan_magenta
- cyan_red
- cyan_white_magenta
- cyan_white_red
- cyan_white_yellow
- cyan_yellow
- gcbmry
- green_blue
- green_magenta
- green_red
- green_white_blue
- green_white_magenta
- green_white_red
- green_white_yellow
- green_yellow
- green_yellow_red
- magenta_blue
- magenta_cyan
- magenta_green
- magenta_white_blue
- magenta_white_cyan
- magenta_white_green
- magenta_white_yellow
- magenta_yellow
- rainbow
- rainbow2
- rainbow2_rev
- rainbow_cycle
- rainbow_cycle_rev
- rainbow_rev
- red_blue
- red_cyan
- red_green
- red_white_blue
- red_white_cyan
- red_white_green
- red_white_yellow
- red_yellow
- red_yellow_green
- rmbc
- yellow_blue
- yellow_cyan
- yellow_cyan_white
- yellow_green
- yellow_magenta
- yellow_red
- yellow_white_blue
- yellow_white_green
- yellow_white_magenta
- yellow_white_red
- yrmbcg
Examples
Simple
spectrum b, blue_red, minimum=10, maximum=50
spectrum count, rainbow_rev, chain A, byres=1
Non-numerical property (Since PyMOL 1.6):
spectrum chain
Custom color list (Since PyMOL 1.6):
spectrum b, blue yellow cyan neon pink grey
Intermediate
The following script will create this image:
# color atoms based on their distance from a point
# returns the length of the distance between atom A and atom B
diff_len = lambda x,y : math.sqrt((x[0]-y[0])*(x[0]-y[0]) + (x[1]-y[1])*(x[1]-y[1]) + (x[2]-y[2])*(x[2]-y[2]))
# fetch 1hug from the PDB
fetch 1hug, async=0
# show it as surface
as surface
# create the pseudoatom at the origin
pseudoatom pOrig, pos=(0,0,0), label=origin
# these are special PyMOL variables that will hold # the coordinates of
# the atoms and the pseudoatom
stored.origCoord = []
stored.distCoord = []
# copy the coordinates into those special variables
iterate_state 1, pOrig, stored.origCoord.append((x,y,z))
iterate_state 1, 1hug, stored.distCoord.append((x,y,z))
# extend origCoord to be the same length as the other
stored.origCoord *= len(stored.distCoord)
# calculate the distances
newB = map(lambda x,y: diff_len(x,y), stored.distCoord, stored.origCoord)
# put them into the b-factor of the protein
alter 1hug, b=newB.pop(0)
# color by rainbow_rev or any other
# palette listed in "help spectrum"
spectrum b, rainbow_rev, 1hug