I want to calculate the diameter of a molecule. Can I do an ellipsoid fitting with Ballview. Or is there any other user friendly software that can do this job? Or also measuring distances etc?
Hello Maria,
I have never used the Ballview software, but I have used PyMol (http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol) to perform this kind of calculations/measurements.
There are some scripts that can be used to calculate the Center Of Mass of a given molecule (http://www.pymolwiki.org/index.php/center_of_mass) an also the radius of giration (http://pymolwiki.org/index.php/Radius_of_gyration), and all these calculations are displayed in the main window. This software also allows to measure distances, angles, etc.
Hope this helps,
Best reagards
Vicente
I would use VMD. After loading your molecule, press 2, and select the two ends of the molecule and the distance in angstrom will output on the screen.
Dear Maria,
The best approach to get the three dimensions of a molecule is to draw it in ArgusLab program (free download), minimize it with molecular mechanics, then with semi-empirical method such as AM1. Once done, you can view it using the same program (ArgusLab) and there is a key for giving you the three dimensions of the molecule (x, y and z). Using the same program you can click any two atomes connected or not connected to get the interatomic distance between them.
Another program called MOLDEN (free download); you can view your optimized structure from Gaussian or ArgusLab in MOLDEN then you click in any two atoms to get the interatomic distance.
It does not matter if the atoms are shown as, balls, sticks or ellipsoid, always you get the same value.
Hoping this will be helpful,
Rafik
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