> >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 > >
Hi Bob, Sorry, I'm not familiar with jmol. I don't understand were to write that command. I'm using jmol as a GUI application under Windows and I load the file by clicking File>Open in the program menu. However the problem is not in opening the file. The format is recognized and spheres are displayed in the correct positions. The only problem is their radii that are not connected to the values written in the pqr file, but they seem absolutely random. Meanwhile I made a new discovery. If I open Preferences there is a slider by which I can modify the percentage of Van der Waals radii. When I slide it from left (0%) to right (100%) the spheres increase in size but when they reach a given size they pop (disappear) and a new sphere starts to grow from zero. It seems like there is a size limit in atom radius...... > > > >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
