Growing Peptides Again

(peptideanimation "peptidechain.gif" (take 17 aminos) :width 2000 :height 1000)

A few small updates to my peptide viz tool (described earlier).

This GIF simply takes each peptide fragment (1; 1,2; 1,2,3…), calculates the structure, and concatenates the images to give an effect of the peptide growing. Obviously its not perfect, however, you can see that CDK’s layout has improved so that the peptide side chains no longer clash. You can also note how the longest carbon chain is detected so that sometimes the terminal side-chains are included as part of linear chain, causing the chain to “bend”.

Might there be a way to spoof a better layout? Perhaps calculating the structures for each incoming amino acid and translate/rotate the end into position might work. Alternatively, keeping the positions from the positions from the previous peptide and rotate/translate each successive image so that the starting peptide location, for example, will always be the same. I think that will be as jerky as this version.

The nice highlight colors are courtesy of CDK-depict.