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(Created page with "===Code=== def colorByDistance(anchor='anchor', site='site'): #Based on: https://pymolwiki.org/index.php/Spectrum#Intermediate #Author: Zhenting Gao (zhentgpicasa@gmail.com)...") |
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| − | ===Code== | + | {{Infobox script-repo |
| + | |type = script | ||
| + | |author = [[User:zhentg|Zhenting Gao]] | ||
| + | }} | ||
| + | == Introduction == | ||
| + | Color the surface of a binding site by the distance to a specific atom. | ||
| + | |||
| + | == Usage == | ||
| + | *Open PyMOL | ||
| + | *Load PDB files | ||
| + | *run this Python script inside PyMOL | ||
| + | *call the function | ||
| + | **colorByDistance anchor, bindingSite | ||
| + | |||
| + | == Required Arguments == | ||
| + | Text | ||
| + | |||
| + | == Optional Arguments == | ||
| + | Text | ||
| + | |||
| + | == Examples == | ||
| + | Text | ||
| + | == The Code == | ||
| + | <source> | ||
def colorByDistance(anchor='anchor', site='site'): | def colorByDistance(anchor='anchor', site='site'): | ||
#Based on: https://pymolwiki.org/index.php/Spectrum#Intermediate | #Based on: https://pymolwiki.org/index.php/Spectrum#Intermediate | ||
| Line 5: | Line 28: | ||
#Update: 11/12/2018 | #Update: 11/12/2018 | ||
#Aim: Color atoms of a binding site based on their distance from a point | #Aim: Color atoms of a binding site based on their distance from a point | ||
| + | #May also refer to https://pymolwiki.org/index.php/Ramp_New#Ramp_.2B_Distance_Measure | ||
# returns the length of the distance between atom A and atom B | # returns the length of the distance between atom A and atom B | ||
| Line 19: | Line 43: | ||
# create the pseudoatom at the origin | # create the pseudoatom at the origin | ||
| − | + | cmd.pseudoatom("pOrig", anchor, label="origin") | |
# these are special PyMOL variables that will hold # the coordinates of | # these are special PyMOL variables that will hold # the coordinates of | ||
| Line 29: | Line 53: | ||
# copy the coordinates into those special variables | # copy the coordinates into those special variables | ||
| − | cmd.iterate_state(1, | + | cmd.iterate_state(1, "pOrig", 'stored.origCoord.append((x,y,z))') |
cmd.iterate_state(1, site, 'stored.distCoord.append((x,y,z))') | cmd.iterate_state(1, site, 'stored.distCoord.append((x,y,z))') | ||
| Line 39: | Line 63: | ||
stored.newB = map(lambda x,y: diff_len(x,y), stored.distCoord, stored.origCoord) | stored.newB = map(lambda x,y: diff_len(x,y), stored.distCoord, stored.origCoord) | ||
| − | print(stored.newB) | + | #print(stored.newB) |
# put them into the b-factor of the protein | # put them into the b-factor of the protein | ||
| − | cmd.alter( | + | cmd.alter( site, "b=stored.newB.pop(0)") |
# color by rainbow_rev or any other | # color by rainbow_rev or any other | ||
| Line 50: | Line 74: | ||
cmd.set("surface_color","-1",site) #color the surface of the binding site by corresponding atom colors | cmd.set("surface_color","-1",site) #color the surface of the binding site by corresponding atom colors | ||
cmd.extend('colorByDistance', colorByDistance) | cmd.extend('colorByDistance', colorByDistance) | ||
| − | |||
</source> | </source> | ||
Latest revision as of 03:24, 10 December 2018
| Type | Python Script |
|---|---|
| Download | |
| Author(s) | Zhenting Gao |
| License | |
Introduction
Color the surface of a binding site by the distance to a specific atom.
Usage
- Open PyMOL
- Load PDB files
- run this Python script inside PyMOL
- call the function
- colorByDistance anchor, bindingSite
Required Arguments
Text
Optional Arguments
Text
Examples
Text
The Code
def colorByDistance(anchor='anchor', site='site'):
#Based on: https://pymolwiki.org/index.php/Spectrum#Intermediate
#Author: Zhenting Gao (zhentgpicasa@gmail.com)
#Update: 11/12/2018
#Aim: Color atoms of a binding site based on their distance from a point
#May also refer to https://pymolwiki.org/index.php/Ramp_New#Ramp_.2B_Distance_Measure
# 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 site from the PDB
#fetch site, async=0
# show it as surface
#as surface
# create the pseudoatom at the origin
cmd.pseudoatom("pOrig", anchor, 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
cmd.iterate_state(1, "pOrig", 'stored.origCoord.append((x,y,z))')
cmd.iterate_state(1, site, 'stored.distCoord.append((x,y,z))')
# extend origCoord to be the same length as the other
stored.origCoord *= len(stored.distCoord)
# calculate the distances
stored.newB = map(lambda x,y: diff_len(x,y), stored.distCoord, stored.origCoord)
#print(stored.newB)
# put them into the b-factor of the protein
cmd.alter( site, "b=stored.newB.pop(0)")
# color by rainbow_rev or any other
# palette listed in "help spectrum"
cmd.spectrum(expression="b", palette="rainbow", selection=site)
cmd.set("surface_color","-1",site) #color the surface of the binding site by corresponding atom colors
cmd.extend('colorByDistance', colorByDistance)