Hi George,
You might want to use cmd.get_model() to make your life easier. It turns a
selection into a chempy model, which has an attribute .atom, containing all
the corresponding atoms with names, identifiers, coordinates, etc.
Check scripts on the pymolwiki that do comparable things.
Hope it h
Dear Leila,
Here is the description of PDB format.
http://deposit.rcsb.org/adit/docs/pdb_atom_format.html#ATOM
Looking at first lines of your pdb file, I think no segid defined in
your pdb file.
So, please try "/com.pdb//a/2/ca" or "com.pdb and chain a and resi 2
and name ca".
Cheers,
Keitaro
I suppose you could modify this script to show sticks when you find a H-bond
pair. Delete the parts that make the dashed line and label and replace them
with "show sticks" or add them to a selection.
http://www.ebi.ac.uk/~gareth/pymol/downloads/scripts/hbond.py
Not the nicest solution, but maybe
Doug,
> select oxy, name o*
should be
select oxy, elem o
FYI: The very latest betas have wildcards enabled for atom names, so in fact
your original idea will work in future PyMOL versions.
http://www.delsci.com
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scienti
