Dear Warren
thanks for that tip - my cylinders look fine now and render
nicely.
best wishes and regards,
Martyn
On Wed, 11 May 2005, Warren DeLano wrote:
> Date: Wed, 11 May 2005 07:27:34 -0700
> From: Warren DeLano <war...@delanoscientific.com>
> To: 'T.A.Wassenaar' <t.a.wassen...@rug.nl>,
> 'Martyn Symmons' <mar...@cryst.bioc.cam.ac.uk>
> Cc: pymol-users@lists.sourceforge.net
> Subject: RE: [PyMOL] cgo cylinders with flat ends? More details
>
> > Maybe it would be nice
> > if there would be a setting like cgo_quality to enhance such
> > a view without rendering.
>
> makes no sense, but the cgo ylinder quality is bound to stick_quality:
>
> set stick_quality, 24
>
> *before* loading the cgo object.
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942 Tech:(650)-872-0834
> . Fax:(650)-872-0273 Cell:(650)-346-1154
> . mailto:war...@delsci.com
>
>
> > -----Original Message-----
> > From: pymol-users-ad...@lists.sourceforge.net
> > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> > T.A.Wassenaar
> > Sent: Wednesday, May 11, 2005 4:12 AM
> > To: Martyn Symmons
> > 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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> > >>
> > >
> > > 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).
