Hi Adam, You could script this using the angle command with specific selections.
Cheers, -- Jason On Wed, Apr 6, 2011 at 11:49 AM, H. Adam Steinberg <a...@steinbergs.us> wrote: > Jason (or someone else), > Is there way in pymol to look for the following angle in a structure φ=-49o > and ψ=-26o ? Which is the definition of a 310 helix. And yes we'd have to > search for a few degrees plus of minus of those angles. They should all > appear in tight turns and last for about 3 or 4 amino acids (I don't think > there wouldn't be any cartoon helix shown). > I don't think there are any pdbs yet that contain pi helices (because of the > loose packing and steric hindrance of the side chains), does anyone know of > any? > Thanks > Adam > On Apr 6, 2011, at 8:16 AM, Jason Vertrees wrote: > > Hi Ramiro, > > PyMOL doesn't differentiate helices, so it cannot color them > differently. If you had the residue labels from some other program > you could read them in and then color by type. > > Cheers, > > -- Jason > > On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz <urcind...@gmail.com> > wrote: > > Hi and thanks for reading this. > > I have googled for a way to achieve what I want and have gone through > > the wiki, to no avail. > > I would like to color in a different way the different helix types: > > alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get > > distinct colors for each type by default. But if the same pdb file is > > open with PyMOL all helices are treated the same way. Can't PyMOL > > distinguish helix types? > > Thanks in advance, > > Ramiro Téllez Sanz > > Dept. Physical Chemistry > > University of Almeria > > Spain > > ------------------------------------------------------------------------------ > > Xperia(TM) PLAY > > It's a major breakthrough. An authentic gaming > > smartphone on the nation's most reliable network. > > And it wants your games. > > http://p.sf.net/sfu/verizon-sfdev > > _______________________________________________ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > > > > -- > Jason Vertrees, PhD > PyMOL Product Manager > Schrodinger, LLC > > (e) jason.vertr...@schrodinger.com > (o) +1 (603) 374-7120 > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > artforscience > H. Adam Steinberg > Artist, Scientist, Developmental Editor > www.artforscience.com > 7904 Bowman Rd > Lodi, WI 53555 > 608/729-5944 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
