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A simple PyMol representation.  Use
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= Overview =
<code>
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A simple PyMol representation where bonds are drawn as sticks.  Use
show sticks, SELECTION
+
<source lang="python">
</code>
+
# using the show command, for some SELECTION
 +
show sticks, SELECTION
 +
 
 +
# using the as command
 +
as sticks, SELECTION
 +
</source>
 
where SELECTION is a valid selection or previously defined selection name.
 
where SELECTION is a valid selection or previously defined selection name.
  
[[Image:Sticks_ex.png|thumb|center|Example Sticks Representation]]
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<gallery>
 +
Image:Sticks_ex.png|Example Sticks Representation
 +
</gallery>
 +
 
 +
==Settings==
 +
*[[stick_ball]]         
 +
*[[stick_nub]]           
 +
*[[stick_transparency]]
 +
*[[stick_ball_ratio]]   
 +
*[[stick_overlap]]       
 +
*[[stick_valence_scale]]
 +
*[[stick_color]]         
 +
*[[stick_quality]]     
 +
*[[stick_fixed_radius]]  
 +
*[[stick_radius]]
 +
*[[set_bond]]   
 +
 
 +
===Example Settings===
 +
=== Color Sticks===
 +
Use [[set_bond]] to set stick-bond settings, like color:
 +
<source lang="python">
 +
set_bond 1foo and i. XYZ, color red
 +
</source>
  
== Sticks Radius  (Sticks Weight)==
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==== Sticks Radius  (Sticks Weight)====
 
To change the radius for sticks, enter the following:
 
To change the radius for sticks, enter the following:
set stick_radius, VALUE
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<source lang="python">
 +
set stick_radius, VALUE
 +
</source>
 
where  
 
where  
 
  0.0<=VALUE<=1.0
 
  0.0<=VALUE<=1.0
  
'''1.0''' is 100% or full radius
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*'''1.0''' is 100% or full radius
 
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*'''0.0''' is 0% or invisible -- so use at least 0.1 or greater
'''0.0''' is 0% or invisible -- so use at least 0.1 or greater
 
 
 
 
 
 
*The default value is: ~0.3
 
*The default value is: ~0.3
  
==Sticks Transparency==
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====Sticks Transparency====
 
To enable transparency for sticks, enter the following:
 
To enable transparency for sticks, enter the following:
set stick_transparency, VALUE
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<source lang="python">
where  
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set stick_transparency, VALUE
0.0<=VALUE<=1.0
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</source>
 
+
where ''0.0<=VALUE<=1.0''
'''1.0''' is 100% transparent -- so invisible
 
 
 
'''0.0''' is 0% transparent -- so opaque
 
 
 
 
 
Example
 
set stick_transparency, 0.45
 
 
 
  
 +
*'''1.0''' is 100% transparent -- so invisible
 +
*'''0.0''' is 0% transparent -- so opaque
  
 +
<source lang="python">
 +
set stick_transparency, 0.45
 +
</source>
  
 
[[Category:Representations|Sticks]]
 
[[Category:Representations|Sticks]]
 +
[[Category:Sticks]]

Latest revision as of 01:44, 28 March 2014

Overview

A simple PyMol representation where bonds are drawn as sticks. Use

# using the show command, for some SELECTION
show sticks, SELECTION

# using the as command
as sticks, SELECTION

where SELECTION is a valid selection or previously defined selection name.

Settings

Example Settings

Color Sticks

Use set_bond to set stick-bond settings, like color:

set_bond 1foo and i. XYZ, color red

Sticks Radius (Sticks Weight)

To change the radius for sticks, enter the following:

set stick_radius, VALUE

where

0.0<=VALUE<=1.0
  • 1.0 is 100% or full radius
  • 0.0 is 0% or invisible -- so use at least 0.1 or greater
  • The default value is: ~0.3

Sticks Transparency

To enable transparency for sticks, enter the following:

set stick_transparency, VALUE

where 0.0<=VALUE<=1.0

  • 1.0 is 100% transparent -- so invisible
  • 0.0 is 0% transparent -- so opaque
set stick_transparency, 0.45