Hi,
I have some ligand files in mol2 format. For each one I have another
file which contains for each atom electrostatic and vdw interaction
information like:
(es) (vdw)
1 -0.345 5.413
2 0.653 -0.12
...
What I would like to do is the following:
1- load the mol2 file in pymol (this is obvious)
2- create two copies (lig_i_es, and lig_i_vdw) in pymol of the ligand,
with line representation, and label for each atom type; C. H. C.ar, ...
3- for lig_i_es, read for each atom the (es) column, and create a bead
around the atom, it's colour is red for negative values of (es) and blue
for positive ones. There is a gradient of colour depending on the
closeness of the value to zero.
4- same for lig_i_vdw
What is the best way of doing this in pymol? If I knew how to create for
each atom a bead with a concrete radius and a concrete color and
gradient, the problem would be solved for me, as I would write an
external pymol script that would prepare the pymol script. I wonder then
which are the commands for craeting this kind of spheres. I also wonder
if there is a more effective way of doing this.
Thanks
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