RE: [PyMOL] Electrostatic potential surface?

[DeLano, W. <wa...@su...>]

> From: Eric C. Peterson [mailto:ec...@ua...]

> I am putting some figures together for an upcoming manuscript=20
> and am trying
> to figure out a few details.  Some of the things I want to do may be
> possible, some not.  Here are the questions I have:
>=20
> 1. How do you display electrostatic potential on surface displays?

Not yet directly possible, but that will change soon. The nearest thing
you can achieve is to color by charge. =20

> 2. Can the colors of individual side chains be changed=20
> without affecting the
> surface?

If you want a uniform surface color,

set surface_color, <color-name>, <object-name>

For anything complicated, just create a second copy of the object.  Show
the surface in one and sticks in the other.  Then color independently.
=20
> 3. I have tried to assign SS manually, but the cartoon skips=20
> at certain
> sections (ie alpha helices).  What can I do to fix this?

Hmm.  This should happen unless those atoms are HETATMS.  To be sure:

show cartoon
alter all,type=3D'ATOM'
rebuild

I'm a little suspicious that there might be some lingering bugs in the
ribbon code.  If you have an example PDB file and script which
reproduces the problem, please send them to me.