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 > > > > > >
