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2014-03-28T01:31:17Z

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= Overview =
[[:Category:CGO|CGO]] cylinders are compiled graphics cylinder objects. If you set the cylinder height to something very small, you can mimic a circle (see examples).
<center>
<gallery heights=300px widths=400px perrow=2>
Image:CylCGO.png|Example cylinder and label. The label was added as a label on a [[Pseudoatom]].
Image:Cylsphere.png|Cylinder with a very thin cyilnder, here 0.2 Angstroms tall to mimic a circle. The label was added as a label on a [[Pseudoatom]].
</gallery>
</center>

= Examples =
<source lang="python">
# Cylinder #1 on left.
x1,y1,z1 = 10, 0, 0 # start point
r1,g1,b1 = 1,0,0 # color (red)
x2,y2,z2 = 0.1, 0, 0 # end point
r2,g2,b2 = 1,1,0 # color (yellow)
radius = 10
cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "cylinder1" )

# Cylinder #2 (the circle)
x1,y1,z1 = -0.1, 0, 0 # start point
r1,g1,b1 = 1,0,0 # color (red)
x2,y2,z2 = 0.1, 0, 0 # end point
r2,g2,b2 = 1,1,0 # color (yellow)
radius = 10
cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "cylinder2" )

# to make the cylinder transparent, use
cmd.load_cgo( [ 25.0, 0.25, 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], "cylinder1" )
</source>

= Usage =
<source lang="python">
cmd.load_cgo( [ a1, a2, cylSpec, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], objName )
</source>
The parameters are:

'''a1, a2'''
:: a1=25 means 'ALPHA' (if you do '''from pymol.cgo import *''' you can then use CGO keywords, like ALPHA, CYLINDER, etc. So, if a1="25.0" then set a2 to some value in the range 0-1.
'''cylSpec'''
:: Cylinder specification: set this to 9.0 or if you did '''from pymol.cgo import *''' you can then use "CYLINDER", here.
'''x1, y1, z1'''
:: coordinates for one end of the cylinder
'''x2, y2, z2'''
:: coordinates for one end of the cylinder
'''radius'''
:: radius of the cylinder
'''r1, b1, g1'''
::color one, (a triplet of values in the range 0-1
'''r2, b2, g2'''
::color two, (a triplet of values in the range 0-1; this allows a gradient
'''objName'''
::Name of cylinder object in PyMOL

= References =
PyMOL list. Thanks to Tsjerk.

[[Category:CGO]]

CGOCylinder - Revision history

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