I want to visualize a random sphere packing. They are not atoms, just generic
spherical particles but I don't know a suitable software to do it so I thougth
I could use jmol.
I have a file with lines in the following format:
x y z r
where x,y,z are the coordinates of the centers of the spheres, which are
contained in a cubic box, and r are the radii (different for each sphere).
Since jmol can read pqr files, which are a modification of pdb files where the
last column is the atom radius, I converted my output file to a "pseudo pqr"
file.
Here an example of a few lines from my pqr file:
ATOM 1 X THR 1 -403.3 -445.3 -72.6 0.00000 20.9
ATOM 2 X THR 1 429.2 285.4 -132.2 0.00000 11.6
ATOM 3 X THR 1 -304.5 -270.2 351.6 0.00000 49.0
ATOM 4 X THR 1 292.5 -208.9 -35.7 0.00000 20.5
ATOM 5 X THR 1 -175.3 4.3 -103.2 0.00000 54.1
(currently coordinates range from -500 to +500, but they can be easily rescaled
if required)
The problem is that when I select Display-Atom-100% Van der Waals I obtain
spheres with radii which are absolutely random and not the values written in
the pqr file...
where is the mistake?
Thank you in advance
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