I'm writing a function script in Python for PyMOL and I need to convert an
atoms number to its location, or somehow gain a list of atom locations form
a group location.
When the script is ran and the function is used the atom locations are
entered :
GKDistance(GLY`730/*,LYS`115/N*)
If I
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
Dear pymol users
I read in the tutorial:
Atom Selection Macros
/object-name/segi-identifier/
chain-identifier/resi-identifier/name-identifier
I don't understand segi-identifier
I want to select a atom *ca* in residue *2* in chain *a* in *com.pdb*.
object-name = com.pdb
*segi-identifier = ?*
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
Hi All-
Is it possible to select all oxygen atoms (backbone sidechain) with a
command similar to the following:
select oxy, name o*
I cannot seem to get any variation of that to work without specifying
all atoms (e.g. o+oe1+oe2)
Thanks,
Doug
