suggestions for Molecules app

I finally got the app to display structures other than the four that come with it, including our own. The secret was to use keywords instead of the 4-digit pdb code, which continues not to work (for me).

The program really works very well. Here are a few suggestions to make it even more useful:

Add an option to display the alpha carbon backbone only. This will make the rendering, rotation etc much faster and the structures more easy to see. Displaying all the atoms is distracting and almost useless for protein molecules larger than insulin.

The "cylinders" option is great and much faster than "balls and sticks" , also the amino acids are coloured by name. It would be very useful if they could be colured by type and functionality, e.g. acidic sidechains (Asp and Glu) red; basic sidechains (Lys, Arg) blue, hydrophobic (Gly, Ala, Val, Leu, Ile, Pro) white; aromatic sidechains (Phe, Tyr, Trp, His) violet; polar sidechains (Ser, Thr, Gln, Asn) light blue; Cys yellow, Met green. This colour code is only a suggestion, but it follows a commonly used convention. In combination with the spacefilling option, this would then also give a good impression of charged areas on the protein surface.

These two fixes should be fairly straightforward.

For a later version, it would be nice if different protein chains and bound cofactors could be painted different colours by the user, and if ribbon diagrams could be drawn (e.g. in rainbow colours from N to C terminus, another convention) and rotated.

I think it is wonderful that the application is freel, and it would be great to keep it like that. On the other hand, many professionals (including myself) would be happy to pay for a version that included the above features, and others (I'd be happy to make further suggestions). Perhaps you can keep a light version that is free, and add a more embellished version for professional scientists and interested amateurs.

Thanks for this wonderful application, and keep up the great work!

WK