To convert a MacroModel file, type
mm2pov [input file ] [output file]
The input file can be any Macromodel data file, although only the first structure will be converted for multi-structure files. The output file should be given the extension '.pov' (although this is not done automatically).You can now run POV with
povray +i[filename] +d
for a test run and
povray highres +i[filename] +d
for the final high-resolution antialiased image. This will create a file called [filename].tga which can then be converted to GIF or JPEG or whatever using your favourite image manipulation program. You can change the size and quality of the generated image by giving POV other options: type 'povray' for a quick summary of options, type 'man povray' for some more in-depth help, or look at the on-line documentation.
The molecule will appear in the same orientation as in MacroModel. However, you have to be aware that by default MacroModel rotates the viewpoint, not the molecule. To rotate the molecule into the correct orientation, restart MacroModel, load your molecule, and rotate that molecule with the TRMol button. Do not rotate the global viewpoint. Save when the molecule is in an orientation you like.
For scenes with multiple molecules (such as receptor-ligand complexes), select all of the molecules separately with TRMol then rotate all of them together by selecting TRAll and a molecular handle.
If you want to change the lighting, scaling, or smoothness or otherwise alter the view settings, then copy all the files in /usr/local/povray3/mm2pov to the directory that your POV files are in. These files are:
atoms.inc - atom definitions (colours, VDW radii etc.)
backgr.inc - the background for the molecule
camera.inc - the camera position
lights.inc - the position, intensity and colour of the lights
You can change the smoothness of the VDW surface by editing the SMOOTH parameter in 'atoms.inc'. A value of 1.001 will give perfectly spherical atoms, while higher values will cause increased blending between adjacent atoms into a molecular envelope. Values of 1.1 to 2 are recommended.
You can change the size of the envelope by altering the VDW_FACTOR value in 'atoms.inc'. This changes the effective VDW radius of the atoms. A value of 0.5 or so gives a sort-of-ball-and-stick representation.
Other aspects of the scene can be changed by editing the various include files. The default viewing geometry is the camera along the positive Z axis, looking in the negative Z direction at the origin. The positive Y axis is towards the top of the screen, the positive X axis is towards the right of the screen (this is a the opposite geometry to the POV default, so be careful).
mm2pov was written by
Mark Mackey (mdm1004@cus.cam.ac.uk)
