Dear Robert,
I have just built the latest PyMOL 1.8.2.0 on CentOS 7, I started it:
pymol -R
and then I ran the following Python script:
#!/usr/bin/env python
import os
import rdkit
from rdkit import Chem
from rdkit.Chem import PyMol
from rdkit.Chem import AllChem
s = PyMol.MolViewer()
mol = Chem.MolFromSmiles \
('CCOCCn1c(C2CC[NH+](CCc3ccc(C(C)(C)C(=O)[O-])cc3)CC2)nc2ccccc21')
mol = AllChem.AddHs(mol)
AllChem.EmbedMolecule(mol)
AllChem.MMFFOptimizeMolecule(mol)
s.ShowMol(mol, name = 'bilastine', showOnly = False)
s.Zoom('bilastine')
s.SetDisplayStyle('bilastine', 'sticks')
I obtained the expected display:
Cheers,
p.
On 04/22/2016 09:09 PM, Robert DeLisle wrote:
Back again!
I apologize for resurrecting an old topic, but I'm once again trying
to work with PyMOL through RDKit. I've been following the approach in
this thread
(http://www.mail-archive.com/rdkit-discuss%40lists.sourceforge.net/msg00325.html)
but it seems not to work any longer. I'm using PyMOL 1.8 on Fedora
and I see that the xml-rpc file is current, so that's no longer a
problem. When I step through the process and hit this step:
s.ShowMol(m,name='ligand',showOnly=False)
nothing happens in the PyMOL viewer. It just remains blank.
Any updates on operating with PyMOL?
-Kirk
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