ColorByGroup - Revision history

Cchem: 3 revisions

2018-12-10T03:24:45Z

3 revisions

Zhentg: /* The Code */

2018-11-12T09:54:36Z

The Code

Zhentg: /* The Code */

2018-11-12T06:47:06Z

The Code

Zhentg: Created page with "{{Infobox script-repo |type = script |author = Zhenting Gao }} == Introduction == Color the objects by their groups. == Usage == Open PyMOL Load PD..."

2018-11-12T06:42:01Z

Created page with "{{Infobox script-repo |type = script |author = Zhenting Gao }} == Introduction == Color the objects by their groups. == Usage == *Open PyMOL *Load PD..."

New page

{{Infobox script-repo
|type = script
|author = [[User:zhentg|Zhenting Gao]]
}}
== 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 ==
<source>
def colorByGroup():
#Based on: https://pymolwiki.org/index.php/Get_Names#ARGUMENTS
#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
groups=cmd.get_names("group_objects")
numClusters=len(groups)
import math
for x in range(numClusters):
colorCode=x*int(math.floor(255/numClusters))
util.cba(colorCode,groups[x])
print(colorCode,groups[x])
cmd.extend('colorByGroup', colorByGroup)
</source>

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

@@ Line 23: / Line 23: @@
 == The Code ==
 <source>
-def colorByGroup():
+def colorByGroup(palette="rainbow"):
 	#Based on: https://pymolwiki.org/index.php/Get_Names#ARGUMENTS
 	#Author: Zhenting Gao (zhentgpicasa@gmail.com)
@@ Line 33: / Line 33: @@
 	import math
 	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)
 </source>

@@ Line 27: / Line 27: @@
 	#Author: Zhenting Gao (zhentgpicasa@gmail.com)
 	#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
 	groups=cmd.get_names("group_objects")

ColorByGroup - Revision history

Cchem: 3 revisions

Zhentg: /* The Code */

Zhentg: /* The Code */

Zhentg: Created page with "{{Infobox script-repo |type = script |author = Zhenting Gao }} == Introduction == Color the objects by their groups. == Usage == *Open PyMOL *Load PD..."

Zhentg: Created page with "{{Infobox script-repo |type = script |author = Zhenting Gao }} == Introduction == Color the objects by their groups. == Usage == Open PyMOL Load PD..."