Hey Osvaldo,
I wasn't sure whether it was COG or COM. For a ligand it may matter. For a
macromolecule it won't. That's easy to see by considering the COM as the
weighted average of the COGs per atom type. Because the distributions will
be pretty much the same in all directions, the COGs will be ap
Hi,
Tsjerk you are right pseudoatom puts a new atom on the geometric center of
a selection.
Just a clarification, the center of mass and the geometric center (AKA
centroid) are not exactly the same thing. The geometric center is the
average of the coordinates and the center of mass is the mass-wei
Hi,
AFAIK, pseudoatom puts a new atom on the center of mass (or geometry) of
the selection. So,
import glob
from pymol import cmd
for pdb in glob.glob("*.pdb"): cmd.pseudoatom(pdb[-3:],"{} and resn
LIGANDNAME".format(pdb))
Or along those lines. Be creative :)
Cheers,
Tsjerk
On Tue, Sep 15,
Hi Raag,
Did pymol crash (quit) with a PDB file written by Gromacs? That can (I
think) only happen if the PDB file is corrupted, for example by coordinates
going out of bound during a simulation. What did you do to obtain the PDB
file?
Cheers,
Tsjerk
On Tue, Sep 15, 2015 at 7:20 AM, Raag Saluja
Hello:
I've got a ligand .sdf file which contains many informations such as:
molecule weight, logP, surface area and so on. I am just wondering is it
possible to display those properties in Pymol?
Thank you very much
Albert
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