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).