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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. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco 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