Difference between revisions of "ColorByDistance"

From PyMOLWiki
Jump to: navigation, search
(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)...")
 
Line 1: Line 1:
 
===Code===
 
===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

Revision as of 01:23, 12 November 2018

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
	# 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

	#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 

	cmd.iterate_state(1, anchor, '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)