POV-Ray, Mol2Mol and Chemistry

For those who have been a bit acquinted with computer graphics, the program Persistence of Vision Ray Tracer (POV-Ray) is surely well-known. This program allows the user to generate three dimensional, photo-realistic images. A detailed description would be too lengthy here, you can find more info on its homepage (www.povray.org). As with computer graphics in general, you can create not only serious scientific illustrations, but surrealistic or funny images as well. Next you can find a few examples of both ones. The original molecule files were transformed to the POV-Ray files with the program Mol2Mol. The fancy images were trimmed manually until they got their final form.

The Mol2Mol 5.6 molecule file conversion and manipulation utility program can recognise and input/output about 40 different types of molfiles. Several utilities are also included.

The following options are available when generating POV-Ray input files:

  • can generate POV-Ray *.pov input files in vector, ball-and-stick and CPK format;
  • optionally generates single, double, triple bonds, and dashed or dotted special bonds;
  • gradient fill coloring of the bonds is supported;
  • coloring according to atom types, residues, chains or models;
  • tubular spline representation of the peptide chains;
  • transparent filling of 3-7 membered rings;
  • gradient coloring by atom partial charges or other atom properties;
  • circles in delocalized planar 5-7 membered rings;
  • to emphasize three-dimensionality, atom size and colouring can be varied by depth;
  • Elemental symbols, atom aliases are supported;
  • calculates the camera and light source objects;
  • Black-and-white pictures for printed illustrations;
  • automatically adds user defined header and footer sections to the *.pov file for the quick and handy generation of the same type of pictures from different molecules;
  • calculates the positions of ground, back or side planes for further effects.

Of course, prior to the generation of a POV-Ray file the molecule can be manipulated with other features of Mol2Mol (add/remove hydrogens, change bond types etc). On the other hand, the file can be endlessly varied in the editor of POV-Ray.

Although there are a few other programs to convert chemistry into POV-Ray images, as far as I know Mol2Mol is the one and only to convert physical or chemical properties into gradient coloring, to calculate the positions of delocalized rings, or to transfer the atom aliases of 2D molecule files.

A few examples follow here. On clicking the pictures you may get bigger, better quality images.



The first image depicts the transition state of an intramolecular Diels-Alder reaction having a half-boat like geometry.





This is the transition state of the addition of an aldehyde to a boronate ester.




This is a planar molecule lying on an orange surface, using area lights.






This image shows an amino acid Cu complex, namely two copper atoms form the complex with two amino acids. The amino acid component is the dimer of penicillamine, connected by a disulfide bridge. Thanks are due to Dr Etelka Farkas for the molecule.




The same molecule with a different rendering.





Three variations for penicillin. I think that penicillin is a well-known compound for everybody, these type of molecules are my favourite ones - I mean their chemistry, of course.




Sorry for this picture card effect.



In this image the penicillin G molecule is coloured by the calculated partial atomic charges (based on AM1 Mullikan point charges).




An aromatic molecule coloured by the electrophilic susceptibility (calculated from the PM3 eigenvectors with CAChe).




You can see here the symmetric HIV-1 protease enzyme (consisting of two chains) with an inhibitor molecule in the active site. The peptide chains are represented as tubular splines.




The oxytocin molecule (a peptide hormone) in crystalline form. The molecule crystallizes as a symmetric dimer with 13 water molecules (below). On the right its backbones are imaged as smoothed splines.


Vancomycin is a special type of peptide antibiotics. The backbone of the molecule consists of unusual amino acids, in addition, the aromatic rings are connected with ether bridges. Vancomycin inhibits the synthesis of the bacterial cell wall, similarly to the penicillins. It is used in severe infections when other antibiotics are ineffective, for example in the case multiresistant MRSA strains or "flesh-eating" bacteria.




A boron derivative with transparently shaded aromatic rings.


Triostin is an antitumor antibiotic, a cyclodepsipeptide with two unusual amino acids including quinoxaline rings capable to intercalate into the DNA: in the complex the aromatic rings (shaded in pink) are inserted into the helix of DNA, parallely with the base pairs of the DNA. In vivo this strongly inhibits the normal function of the DNA.




C-240 fulleren with transparently shaded aromatic rings + delocalized circles, illuminated from inside



A RuCl2 complex using delocalized circles in the aromatic rings.



Iron complex of a haem derivative. Gradient colouring of the bonds is used, and to emphasize the three-dimensionality, the colour is varied by the depth.



Boron subphthalocyanine chloride – using sticks combined with transparent spacefill model.



The taxol (paclitaxel) molecule, as converted from a 2D ISIS/Draw mol file. Taxol was first isolated from the bark of the Pacific yew tree (Taxus brevifolia), and is used for the therapy of breast and ovarian cancer.



Black-and-white images for printed publications   



At last three variations of the C-60 fulleren molecule, buckminsterfulleren follow:


All images © Tamas E. Gunda – 09.02.2009.