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Difference between revisions of "ColorByGroup"

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(Created page with "{{Infobox script-repo |type = script |author = Zhenting Gao }} == Introduction == Color the objects by their groups. == Usage == *Open PyMOL *Load PD...")
 
m (3 revisions)
 
(2 intermediate revisions by one other user not shown)
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== The Code ==
 
== The Code ==
 
<source>
 
<source>
def colorByGroup():
+
def colorByGroup(palette="rainbow"):
 
#Based on: https://pymolwiki.org/index.php/Get_Names#ARGUMENTS
 
#Based on: https://pymolwiki.org/index.php/Get_Names#ARGUMENTS
 
#Author: Zhenting Gao (zhentgpicasa@gmail.com)
 
#Author: Zhenting Gao (zhentgpicasa@gmail.com)
 
#Update: 11/12/2018
 
#Update: 11/12/2018
#Aim: Color atoms of a binding site based on their distance from a point
+
#Aim: Color the objects by their groups.
 
# returns the length of the distance between atom A and atom B
 
# returns the length of the distance between atom A and atom B
 
groups=cmd.get_names("group_objects")
 
groups=cmd.get_names("group_objects")
Line 33: Line 33:
 
import math
 
import math
 
for x in range(numClusters):
 
for x in range(numClusters):
colorCode=x*int(math.floor(255/numClusters))
+
cmd.alter(groups[x],"b="+str(x))
util.cba(colorCode,groups[x])
+
cmd.spectrum( "b", palette, " ".join(groups))
print(colorCode,groups[x])
+
#https://pymolwiki.org/index.php/Spectrum
 
cmd.extend('colorByGroup', colorByGroup)
 
cmd.extend('colorByGroup', colorByGroup)
 +
 
</source>
 
</source>

Latest revision as of 03:24, 10 December 2018

Type Python Script
Download
Author(s) Zhenting Gao
License

Introduction

Color the objects by their groups.

Usage

  • Open PyMOL
  • Load PDB files, create groups
  • run this Python script inside PyMOL
  • call the function
    • colorByGroup

Required Arguments

Text

Optional Arguments

Text

Examples

Text

The Code

def colorByGroup(palette="rainbow"):
	#Based on: https://pymolwiki.org/index.php/Get_Names#ARGUMENTS
	#Author: Zhenting Gao (zhentgpicasa@gmail.com)
	#Update: 11/12/2018
	#Aim: Color the objects by their groups.
	# returns the length of the distance between atom A and atom B
	groups=cmd.get_names("group_objects")
	numClusters=len(groups)
	import math
	for x in range(numClusters):
		cmd.alter(groups[x],"b="+str(x))
	cmd.spectrum( "b", palette, " ".join(groups))
	#https://pymolwiki.org/index.php/Spectrum
cmd.extend('colorByGroup', colorByGroup)