You have to work through the following three points in order to analyse the shape of a molecule or a host cavity. A demo input file with the structure of α-cyclodextrin is available for testing the program.

1. Calculation with Gaussian03
2. Analysing the electron density with the MolShape program
3. Evaluation of the MolShape data (e. g. with OpenOffice Calc)

The MolShape script needs the electron density of the structure as a cube file, produced with the program cubegen. Consult your Gaussian03 manual for further information.

Start the MolShape application...



Choose a cube file by clicking on 'Browse'...



Enter the atom numbers of the start and end atom for the calculation of the profile (9 and 11 for the demo file) and adjust the electron density cut-off if necessary (a common value is 0.002 electrons/bohr³...



Choose the volume mode (3D) and select the axis system (zyx for the demo file)...



Start the calculation by clicking on 'OK'...



Wait until the calculation is finished...



The end of the calculation is indicated by a corresponding dialog...

The evaluation of the data produced by MolShape can be done with nearly any program. In the following the program OpenOffice Calc will be used to visualize the results.

Open the data file produced by MolShape (file extension '_molshape.dat')...



Plot for instance the sixth column (equivradius) as a function of the second column (coordrel)...



You will get the profile of the α-cyclodextrin cavity from the atoms 9 (O-3) to 11 (O-6)...

A detailed description of the MolShape algorithm can be found in my PhD thesis ( PDF file, 3.67 MB). The thesis is written in German, but includes an English abstract. Please feel free to contact me via e-mail (see footer) if you have further questions.