James, FYI: What you're trying to accomplish is impossible with PyMOL -- cartoons only pass through C-alpha positions, not amide C or N. Thus, the only sure way to get the backbone carbonyl connected to the cartoon is to switch PyMOL into Editing Mode and then ctrl-left-click-and-drag the carbon coordinate into the path of the cartoon. Another possible approach would be to make the cartoon larger via the cartoon ..._length, ..._width, and ..._radius settings.
However, my personal view is that if you are close enough to care about amide C & N's, then you shouldn't be using cartoons...they are little more than artistic fancy. 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:[email protected] > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf > Of James Knight > Sent: Sunday, June 04, 2006 6:28 PM > To: Robert Immormino > Cc: [email protected] > Subject: Re: [PyMOL] sticks don't touch backbone > > Thanks for the reply, but no luck. It seems the backbone can > be refined using cartoon_refine, but there is a limit to how > far. Unfortunately in some cases the carbonyl (and the > nitrogen as well) misses be a lot when the area of interest > is zoomed in on. I guess I just have to play with the camera > angle to make it look like the sticks are attached. > > Cheers, > James > > On Sun, 2006-04-06 at 17:25 -0400, Robert Immormino wrote: > > James, > > > > I don't know if this will fix your problem or not, but try: > > > > cartoon_side_chain_helper > > > > Also when smoothing is turned off I think the cartoon is forced > > through the Calpha, and not through all of the backbone > atoms, so it > > is not surprising that the carbonyl misses by a little. > > > > Cheers, > > > > -bob > > > > On 6/4/06, James Knight <[email protected]> wrote: > > > > > > I'm trying to get a stick from the "C" carbon that is > part of the > > > backbone to the "O" it is double bonded to. I use the > command: "show > > > sticks, resi 100 and name c+o". I get a stick that > doesn't touch the > > > backbone. If I turn off all smoothing (set > cartoon_smooth_loops, 0; > > > set cartoon_flat_sheets, 0), the stick still doesn't reach the > > > backbone. It seems there is still a small amount of > smoothing. Is there a way to change this? > > > > > > James > > > > > > > > > _______________________________________________ > > > PyMOL-users mailing list > > > [email protected] > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > > _______________________________________________ > PyMOL-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > >
