Re: [PyMOL] Roving detail and Roving density

[Nathaniel E. <nat...@gm...>]

On Wed, Apr 22, 2009 at 6:37 PM, Craig Smith <boi...@ma...> wrote:

> I was looking at the demos in pymol (wizard --> demo) and saw
> interesting features called roving detail and roving density.  I
> looked in the manual on how to do this feature but couldn't find it.
> Could anyone point me in the right direction or show me how to
> interactively display electron density as I move through my structure.
>

This is what I do (sorry, it's in Python, but easily converted to PyMOL
commands).  It assumes that you have two maps loaded, named "2fofc" and
"fofc".    (Some of it is cribbed from the C code for the roving density
demo.)

    cmd.set("roving_detail", 20)
    cmd.set("roving_isomesh", 20)
    cmd.set("roving_origin", 1)
    cmd.set("roving_sticks", 0)
    cmd.set("roving_ribbon", 0)
    cmd.set("roving_lines", 0)
    cmd.set("roving_spheres", 0)
    cmd.set("roving_nb_spheres", 0)
    cmd.set("roving_polar_contacts", 0)
    cmd.set("roving_polar_cutoff", 0)
    cmd.set("roving_map1_name", "2fofc")
    cmd.set("roving_map1_level", 1)
    cmd.set("roving_map2_name", "fofc")
    cmd.set("roving_map3_name", "fofc")
    cmd.set("roving_map2_level", 3)
    cmd.set("roving_map3_level", -3)

    cmd.isomesh("rov_m1", "2fofc", 1.0, "center", 20)
    cmd.isomesh("rov_m2", "fofc", 3.0, "center", 20)
    cmd.isomesh("rov_m3", "fofc", -3.0, "center", 20)
    cmd.color("skyblue", "rov_m1")
    cmd.color("green", "rov_m2")
    cmd.color("red", "rov_m3")

This might not be ideal - some of those 'set' commands may be unnecessary or
incorrect.  However, the end result works more or less like Coot, which is
what I was aiming for.

-Nat