> From: Byron DeLaBarre [mailto:by...@slac.stanford.edu] > > Anyone out there know how to prevent bonding of adjacent but > 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=1" or "alter (all),type='ATOM'" followed by "sort" and "rebuild". Same for goes for meshes. > And along those lines, anyone had success with showing a > 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 > 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=1" Warren
