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).
