Dear Tsjerk
thanks for that - I am not using the latest pymol so I will
upgrade and try again.
I will let you know how it goes.
cheers
Martyn
On Wed, 11 May 2005, T.A.Wassenaar wrote:
> Date: Wed, 11 May 2005 13:11:54 +0200
> From: T.A.Wassenaar <t.a.wassen...@rug.nl>
> To: Martyn Symmons <mar...@cryst.bioc.cam.ac.uk>
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] cgo cylinders with flat ends? More details
>
>
> 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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> >> >
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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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>
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).
