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

Daniel Svozil svozil at uochb.cas.cz
Fri Nov 18 06:58:17 PST 2005

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 

I am sure other Chimera users would take a benefit if them too. Of 
course you're right more sophisticated capabilities would probably 
require force field implementation, and I understand this is 
(unfortunately) not the direction Chimera is heading to.


Daniel Svozil, PhD
Institute of Organic Chemistry and Biochemistry
Center for Biomolecules and Complex Molecular Systems
Czech Republic

phone: +420-220 410 312

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