# CGOCylinder

## Contents

# Overview

CGO cylinders are compiled graphics cylinder objects. If you set the cylinder height to something very small, you can mimic a circle (see examples).

Example cylinder and label. The label was added as a label on a Pseudoatom.

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.

# Examples

```
# 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" )
```

# Usage

```
cmd.load_cgo( [ a1, a2, cylSpec, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2, g2, b2 ], objName )
```

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.

- a1=25 means 'ALPHA' (if you do

**cylSpec**

- Cylinder specification: set this to 9.0 or if you did
**from pymol.cgo import ***you can then use "CYLINDER", here.

- Cylinder specification: set this to 9.0 or if you did

**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.