ColorByDistance - Revision history

Cchem: 5 revisions

2018-12-10T03:24:44Z

5 revisions

Zhentg: /* The Code */

2018-11-12T10:08:15Z

The Code

Zhentg at 06:35, 12 November 2018

2018-11-12T06:35:31Z

Zhentg at 06:33, 12 November 2018

2018-11-12T06:33:08Z

Zhentg at 06:23, 12 November 2018

2018-11-12T06:23:43Z

Zhentg: 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)..."

2018-11-12T06:23:07Z

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)..."

New page

===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)

</source>

@@ Line 3: / Line 3: @@
 |author    = [[User:zhentg|Zhenting Gao]]
 }}
-==Code==
+== Usage ==
 <source>
 def colorByDistance(anchor='anchor', site='site'):

@@ Line 1: / Line 1: @@
-===Code===
+{{Infobox script-repo
 <source>
 def colorByDistance(anchor='anchor', site='site'):

← Older revision	Revision as of 03:24, 10 December 2018
(No difference)

@@ Line 28: / Line 28: @@
 	#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
@@ Line 42: / Line 43: @@
 	# create the pseudoatom at the origin
-	#pseudoatom pOrig, pos=(0,0,0), label=origin
+	cmd.pseudoatom("pOrig", anchor, label="origin")
 	# these are special PyMOL variables that will hold # the coordinates of
@@ Line 52: / Line 53: @@
 	# copy the coordinates into those special variables
-	cmd.iterate_state(1, anchor, 'stored.origCoord.append((x,y,z))')
+	cmd.iterate_state(1, "pOrig", 'stored.origCoord.append((x,y,z))')
 	cmd.iterate_state(1, site, 'stored.distCoord.append((x,y,z))')
@@ Line 62: / Line 63: @@
 	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
-	cmd.alter( "site", "b=stored.newB.pop(0)")
+	cmd.alter( site, "b=stored.newB.pop(0)")
 	# color by rainbow_rev or any other
@@ Line 73: / Line 74: @@
 	cmd.set("surface_color","-1",site) #color the surface of the binding site by corresponding atom colors
 cmd.extend('colorByDistance', colorByDistance)
 </source>