> 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). > >> > > >> > > >> > > >> > > >> > > >>------------------------------------------------------- > >> > 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 > > > ------------------------------------------------------- > 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 >
