Hi Francesco, Yes, you can use Adjust Torsions to rotate several different bonds along the backbone. It might be a lot of work, and it would not prevent you from creating structures with bad contacts, but you could certainly try it if MD alone is not successful in generating the desired conformations. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/struc...

Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On Apr 19, 2009, at 9:56 AM, Francesco Pietra wrote:

I would like to straighten a helix in a complex composition of helices, i.e., at least some of them may vdw interact with each other if moved. Therefore, I plan to let molecular dynamics (MD) changing dihedral angles at the pivot amino acid. I wonder whether chimera might aid through "adjust torsion" or other tool. If not else to provide alternative conformations for input to MD and see if the adjustments converge. Bending of the helix occurs along 5 amino acids, the central one probably the pivot. Thanks francesco pietra _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users