Dear Tsjerk
thanks - you were right - now I have upgraded and they come out
as nice flat cylinders, looks good.
Thanks again for trying that for me
best wishes and regards
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).
> > >> >
> > >> >
> > >> >
> > >> >
> > >> >
> > >>-------------------------------------------------------
> > >> > This SF.Net email is sponsored by Oracle Space
> > >> >Sweepstakes
> > >> > Want to be the first software developer in space?
> > >> > Enter now for the Oracle Space Sweepstakes!
> > >> >
> > >>http://ads.osdn.com/?ad_id=7393&alloc_id=16281&op=click
> > >> > _______________________________________________
> > >> > PyMOL-users mailing list
> > >> > PyMOL-users@lists.sourceforge.net
> > >> >
> > >>https://lists.sourceforge.net/lists/listinfo/pymol-users
> > >>
> > >>
> > >
> > > 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).
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by Oracle Space
> > >Sweepstakes
> > > Want to be the first software developer in space?
> > > Enter now for the Oracle Space Sweepstakes!
> > > http://ads.osdn.com/?ad_id=7393&alloc_id=16281&op=click
> > > _______________________________________________
> > > PyMOL-users mailing list
> > > PyMOL-users@lists.sourceforge.net
> > > https://lists.sourceforge.net/lists/listinfo/pymol-users
> >
>
> 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).
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by Oracle Space Sweepstakes
> Want to be the first software developer in space?
> Enter now for the Oracle Space Sweepstakes!
> http://ads.osdn.com/?ad_id=7393&alloc_id=16281&op=click
> _______________________________________________
> PyMOL-users mailing list
> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
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).
