Daniel Svozil wrote:
Hi Tom,
If you think specific new model building capabilities would be helpful given the above limitations, explain them and we will be happy to consider them.
For the beginning, I think the following "model building" capabilities would make Chimera even more useful (some of them are maybe already implemented, I do not know Chimera so well yet):
1) Move atom, move selection of atoms, delete selection/atom. Add atoms. 2) Change atom to another one. 3) Add/attach functional groups from library 4) I work in the field of nucleic acids, it would be nice one could build the "ideal" structure (B-DNA, A-DNA, Z-DNA) from sequence (if needed, I can provide a references to papers publishing geometry parameters). Possibly change of pseudorotation angle in deoxyribose and ribose.
For nucleotide polymers, I've wrapped most of X3DNA in Python in my Ensemble.Legacy library. It's highly alpha code, but I've been able to use it to generate X3DNA parameters from PDB files, and adding support for building nucleotide structures with arbitrary X3DNA parameters wouldn't be hard (you give it twist, tilt, roll, etc, and it gives you a PDB structure consistent with those parameters). If I had an infinite number of monkeys, I could probably wrap all that into a Chimera extension that let you build arbitrary structures for DNA/RNA, etc with a nice interface. However, I don't, so all I can do is make the code available on a subversion repository and provide minimal advice on how to build onto it. Dave