Thanks for the suggestion, it led me to the root of my problem. I discovered this morning that my problem was more to do with my understanding of cgo syntax/hierarchy/ordering. Hence
   
    obj.extend([COLOR, 0.8, 0.8, 0.8])  # greyish
    obj.extend([ALPHA, 0.5])
    obj.extend([BEGIN, TRIANGLE_STRIP])

and variations on it, doesn't work. But the below does.

    obj.extend([ALPHA, 0.5])
    obj.extend([COLOR, 0.8, 0.8, 0.8]) # greyish
    obj.extend([BEGIN, TRIANGLE_STRIP])

Cheers,
Robin

DeLano Scientific wrote:
Robin,

Try:

obj.extend([ALPHA,0.5])

Cheers,
Warren

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DeLano Scientific LLC
Subscriber Support Services
mailto:delsci@delsci.info
 

  
-----Original Message-----
From: pymol-users-bounces@lists.sourceforge.net 
[mailto:pymol-users-bounces@lists.sourceforge.net] On Behalf 
Of Robin Owen
Sent: Wednesday, February 06, 2008 8:18 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] transparency of cgo plane

Hi all,

I've been writing a small pymol script based on 
plane_wizard.py from the pymol wiki 
http://www.pymolwiki.org/index.php/Plane_Wizard
(and also Warren's script cgo_plane.py ) However, I'm getting 
stuck with the modification I'd most like to make. 
I'd like the plane to be partially transparent. This seems to 
be possible ( http://delsci.com/img/pore.jpg ) but I think I 
must be overlooking something obvious in cgo syntax...
I found an old message in the archive saying this can only be 
done at the time the object is created using something like

def makeSphere(name, x, y, z, r, transparency=0.5):
obj[]
obj.extend([cgo,1-transparency])
cmd.load_cgo(obj,name,1)

but have had no success in adapting/integrating this.

Thanks in advance for any ideas,
Robin

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