Indeed, Jmol is perfect and has been used like this before. (For, example,
electron probability plots.)
Because PQR and PDB have the same format, you will need to preface your
file name with "pqr::" to force Jmol to read PQR format. If you can scale
your coordinates down by a factor of 50, this would look about the size of
a molecule. But it should work even with this large range.
Bob Hanson
On Thu, Mar 21, 2013 at 1:27 PM, Andrea Magro <[email protected]> wrote:
> 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
>
>
>
>
> ------------------------------------------------------------------------------
> Everyone hates slow websites. So do we.
> Make your web apps faster with AppDynamics
> Download AppDynamics Lite for free today:
> http://p.sf.net/sfu/appdyn_d2d_mar
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Everyone hates slow websites. So do we.
Make your web apps faster with AppDynamics
Download AppDynamics Lite for free today:
http://p.sf.net/sfu/appdyn_d2d_mar
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
