You're welcome! I forgot to mention that for RNA (not DNA), there is a nice modeling/refinement plugin, Assemble2, developed by Fabrice Jossinet at University of Strasbourg: <http://bioinformatics.org/assemble/index.html> It interfaces with web services for RNA structure prediction and refinement. Elaine On Jun 26, 2014, at 11:02 AM, sette@uniroma2.it wrote:
Hi Elaine,
this is very useful :) Many thanks!!! Marco
Elaine Meng <meng@cgl.ucsf.edu> ha scritto:
Dear Marco, There is a "swapna" command for mutating nucleic acids: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapna.html>
The results may be fairly rough, with some nonoptimal geometries and/or steric clashes, but you could try this and see if it meets your needs. There is also a Minimize Structure tool (in menu under Tools... Structure Editing) or "minimize" command, but it has limited ability to clean up a structure.
On Jun 25, 2014, at 1:00 AM, sette@uniroma2.it wrote:
Dear all, I'm interested to create a rough model of a quadruplex molecule using a specific sequence. One possibility could be to load a pdb structure of a quadruplex and « mutate » each nucleotide with the correct one. Is this feasible with Chimera ? Alternative suggestions are appreciated as well. Thanks for your help, Marco