Werner,
First, you can show your ligands as ball-and-stick, by hand:
as spheres
show sticks
set sphere_scale, 0.25, *
set stick_radius, 0.125, *
then set the sphere_radius for each atom based on your values. Here's
an example of fetching the b-factor value from each atom and setting
the sphere_radius based on the scaled b-factor:
fetch 1hpv
from pymol import stored
# set the stored array equal to the b-values; or use your own values
stored.bb = []
iterate *, stored.bb.append(b)
# execute a python-block
python
# scale the b-values
M = max(stored.bb)
scaledBB = map( lambda x: float(x/M), stored.bb)
count = 0
# set the sphere radii independently
for x in scaledBB:
cmd.set("sphere_scale", x, "ID %s" % count)
count = count + 1
python end
Last, for coloring, set your property in the b-value column (see
http://www.pymolwiki.org/index.php/Color#B-Factors, the spectrum
command) and color by b-factor. This is very common, and the
PyMOLWiki is full of examples. If the above script collides with your
b-factor coloring, you can also use the charge 'q' field.
Cheers,
-- Jason
On Fri, Mar 26, 2010 at 8:06 PM, Werner Schroedinger
<werner.schroedinger@...> wrote:
> 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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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) Jason.Vertrees@...
(o) +1 (603) 374-7120
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