> From: Byron DeLaBarre [mailto:byron@...]
> Anyone out there know how to prevent bonding of adjacent but=20
> 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 =
> 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 =