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...") |
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| Line 23: | Line 23: | ||
== 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 | + | #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): | ||
| − | + | cmd.alter(groups[x],"b="+str(x)) | |
| − | + | cmd.spectrum( "b", palette, " ".join(groups)) | |
| − | + | #https://pymolwiki.org/index.php/Spectrum | |
cmd.extend('colorByGroup', colorByGroup) | cmd.extend('colorByGroup', colorByGroup) | ||
| + | |||
</source> | </source> | ||
Latest revision as of 05:54, 12 November 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)