[Chimera-users] Move atoms (selections) in Chimera

[David E. Konerding]

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