RE: [PyMOL] easy (?) question

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

> From: Byron DeLaBarre [mailto:by...@SL...]
>=20
> Anyone out there know how to prevent bonding of adjacent but=20
> chemically
> unconnected atoms in pymol?

Two step process:

1. edit the PDB file and replace "ATOM  " with "HETATM"
2. after the HETATM's add a single record "CONECT" following by nothing =
but a new-line.  This will signal PyMOL to expect explicit connectivity =
(of which there will be none).  In the future, if you need to specify =
connectivity explicitly, this is how you do it using a PDB file (CONECT =
records followed by connectivity info)

Note if you need to surface hetatms, "set surface_mode=3D1" or "alter =
(all),type=3D'ATOM'" followed by "sort" and "rebuild".  Same for goes =
for meshes.

> And along those lines, anyone had success with showing a=20
> Calpha trace?  I
> tried once but couldn't figure out how to get pymol to connect the
> individual Calpha atoms.  I think this must be easy to do =20
> but I couldn't
> work it out at the time.

So long as the N and C atoms are also present, the ribbon representation =
can do this.  It looks for CA atoms three bonds apart to form the trace. =
  To get a linear C-alpha trace (no smoothing), "set =
ribbon_sampling=3D1"

Warren
=20