Hi Vincent,
25.0 is not a cylinder, but a sausage. Since it has a spherical end, it
also has a highlight/phong, which is rendered white and therefore
disappears against your background. This won't just happen, but I guess
that you've set the raytrace and light settings such that it only gives the
two colors.
The code for a cylinder is 9.0. or cgo.CYLINDER
Hope it helps,
Tsjerk
On Thu, Jan 14, 2016 at 11:19 AM, vincent Chaptal <vincent.chap...@ibcp.fr>
wrote:
> Hi all,
>
> I am drawing a cylinder as a cgo in pymol, and it shows a hole after ray
> tracing.
> I attach the image for clarity, shown here from the top.
>
> In fact, this hole shows some time but not always. I haven't found out why
> it is appearing though, so I would appreciate if anyone has an idea on how
> to make it disappear and draw a full cylinder?
>
> bellow is the script used to display it: (I'm using pymol 1.7.4.3 under
> MacOS 10.10.5)
> from pymol.cgo import *
> from pymol import cmd
>
> # Cylinder #1
> x1,y1,z1 = 0, 0, 15.8 # start point
> r1,g1,b1 = 0,1,0 # color (green)
> x2,y2,z2 = 0, 0, -15.8 # end point
> radius = 45.4
> cmd.load_cgo( [ 25.0, 0.5, 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1,
> b1, r1, g1, b1 ], "cylinder1" )
>
>
>
> Thank you for your help.
> vincent
>
>
> --
>
> Vincent Chaptal, PhD
>
> Institut de Biologie et Chimie des Protéines
>
> Drug Resistance and Membrane Proteins Laboratory
>
> 7 passage du Vercors
>
> 69007 LYON
>
> FRANCE
>
> +33 4 37 65 29 01
>
> http://www.ibcp.fr
>
>
>
>
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--
Tsjerk A. Wassenaar, Ph.D.
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