Viewing Proteins with Molecular Modeling Pro
For those wishing to view proteins in the Brookhaven pdf format with Molecular Modeling Pro we recommend that you also download one of the versions of the free program RASMOL. Molecular Modeling Pro can then be used to calculate chemical properties of the proteins and create databases of them, while RASMOL would be used to actually view and rotate the molecules. Molecular Modeling Pro automatically will load you protein viewing program any time a Brookhaven pdf file is opened.
If you have the program ChemSite, it is a good alternative to RASMOL for viewing proteins. ChemSite is a full featured modeling program with 2-D and 3-D drawing features, a minimizer, molecular dynamics simulations and great graphical rendering capabilities. You can order ChemSite from Norgwyn Montgomery if you like. It is not free, but it is very reasonably priced ($99 Academic, $199 regular).
Cooperation between Molecular Modeling Pro and RASMOL or ChemSite is created by selecting "Initialize links" from the Edit menu then typing in the file pathname for the "Protein database viewer" (be it RASMOL or ChemSite).
You can download RASMOL as follows:
Download the executable file and the two help files. You can also download the source code for this program and make you own flavor of RASMOL which was done at the two universities linked below.
UCB enhanced RASMOL from the University of California at Berkeley:
Protein Explorer (enhanced RASMOL at the University of Massachusetts):
We have only tested MMP with RASMOL, but assume that the support for Command line passing of file names is supported in the enhanced versions too.
Chemical properties calculated by Molecular Modeling Pro for proteins include surface area, hydrophilic surface area, percent hydrophilic surface area, dipole moment, polar surface area, dimensions [length, width and depth], van der Waal's volume, hydration number and perhaps some of the synthetic polymer properties, such as the 3-D solubility parameters and chain length. Connectivity indices will be accurately calculated as well. Many of the other properties calculated by MMP will be less useful as the calculation methods were created using smaller molecules, and their accuracy will be suspect.
When creating databases with Molecular Modeling Pro of molecules in the Brookhaven pdf format make sure that you choose to store the structures as pdf files. Do not store them internally in the database or in some other file format. This will insure that valuable information about the proteins is not lost and that the protein viewing program will be able to open the molecules. You cannot modify the structures either without losing some data. Molecular Modeling Pro will allow you to save Brookhaven pdf files, but it saves the structures with only the atom type and connections, losing much valuable information. On the other hand, molecules created with MMP and saved in Brookhaven pdf format can be viewed with RASMOL. The point is that a lot of protein specific information is read in by MMP but not stored in pdf files it creates. When creating databases of pdf files, MMP does not overwrite the pdf files, but creates a field with the file names in it.