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
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
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
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 = ?*
c
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
Hi,
I have been using the dist command with mode=2 to show hydrogen bonds around a
ligand. Is there a way to make a selection of all the residues in a protein
hydrogen bonding with a ligand, so that I can show them as sticks.
Thanks in Advance.
-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Douglas Kojetin
> Sent: Wednesday, April 20, 2005 1:55 PM
> To: 'pymol'
> Subject: [PyMOL] atom selection: wildcard
>
> Hi All-
>
> Is it possible to select all oxygen
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
HI! All:
I am used an old version of pymol. When I selected C5* in the backbone of
DNA , pymol will select two atoms, one is C5* on backbone the other is
C5 on base pair. My expression isselect (chain/residue number/C5*).
If you are using the newly version of pymol, would you like to try the
ex
