Hi Martin,
For me (Suse 9.0 Linux, Pymol 0.98b) this scripts seems to
do exactly what you want. After rendering that is. If the
scene is not rendered, the cylinder is an eight-sided
prism, which is due to the openGL implementation. Maybe it
would be nice if there would be a setting like cgo_quality
to enhance such a view without rendering.
But does your problem persist after rendering, and if so,
could you show an image illustrating that? Though I have
to add that I won't be the one to help from that point on,
as it'll be in the implementation.
Cheers,
Tsjerk
On Wed, 11 May 2005 11:45:36 +0100
Martyn Symmons <mar...@cryst.bioc.cam.ac.uk> wrote:
Dear Tsjerk and other pymolites
To draw my cylinders I just modified Warren's example
from the CGO
demos in the examples/devel directory. I give this
below. Maybe there is
another way to do this? I would like cylindrical
cylinders with sharp cut
ends rather than rounded ends. I guess this is down to
OPENGL not to
pymol.
I have another program that looks at the RNA atomic
coordinate file and
writes in the coordinates of the double-helical regions
of the RNA.
(currently this is based on a user going through the
secondary structure
by hand - I discussed with Luca Jovine a little about
whether it could be
done automatically but he has not time just now to spend
on this).
So below is an example of Warren's code after I hack in
my coordinates,
You get it into pymol by using the 'run' command.
Thanks for any help with this.
Best wishes and regards
Martyn
-------------------------------------------------------------------
# this is a trivial example of creating a cgo object
consisting of a
# a single state
# first we create a list of floats containing a GL
rendering stream
# obj is an empty list to begin with...
obj = []
obj.extend( [ CYLINDER,
13.839,-33.646,20.164,24.5685,-15.6645,16.6015, #hacked
in from coords
10.0,
# Radius
0.0, 0.0, 1.0, # RGB Color 1
0.0, 0.0, 1.0, # RGB Color
2
] )
# then we load it into PyMOL
cmd.load_cgo(obj,'cgo013')
# move the read clipping plane back a bit to that that
is it brighter
cmd.clip('far',-5)
On Tue, 10 May 2005, T.A.Wassenaar wrote:
Date: Tue, 10 May 2005 21:37:33 +0200
From: T.A.Wassenaar <t.a.wassen...@rug.nl>
To: Martyn Symmons <mar...@cryst.bioc.cam.ac.uk>
Subject: Re: [PyMOL] cgo cylinders with flat ends?
Hi Martyn,
It sounds like you used the SAUSAGE keyword rather than
the CYLINDER keyword, the latter of which is a true
cylinder. But if this line of deduction is wrong, please
show what you tried and the result it gave.
Cheers,
Tsjerk
On Tue, 10 May 2005 18:22:10 +0100
Martyn Symmons <mar...@cryst.bioc.cam.ac.uk> wrote:
> dear pymol-users
> I have used CGO to put down 20
>angstrom-wide cylinders on
> the helical bits of a large RNA molecule. They come
out
>with nice rounded
> ends but I would prefer flattened ends if possible. Is
>there any way I can
> do that?
> Thanks for any help/advice.
> cheerio for now,
> Martyn
> Martyn F. Symmons (Ph.D.)
> Research Associate
> Crystallography and Biocomputing Group
> Department of Biochemistry
> University of Cambridge
> Phone: 01223 766020
> -----------------------
> "Abair ach beagan agus abair gu math e"
> Seanfhacal Gaidhlig (Gaelic Proverb).
>
>
>
>
>
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Martyn F. Symmons (Ph.D.)
Research Associate
Crystallography and Biocomputing Group
Department of Biochemistry
University of Cambridge
Phone: 01223 766020
-----------------------
"Abair ach beagan agus abair gu math e"
Seanfhacal Gaidhlig (Gaelic Proverb).
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