Hello Rodrigo, The commands look correct to me. I tried this test to rotate 1gcn Asp-15 CA-CB bond, and it worked to change the angle in both the display and the saved pdb file: open 1gcn display labelopt info serialNumber la @cb,cg rotation 0 @/serialNumber=120 @/serialNumber=121 rotation 0 90 write format pdb #0 ~/Desktop/t1.pdb ~rot 0 write format pdb #0 ~/Desktop/t2.pdb … I wrote the second file because I thought it might be necessary to turn off and freeze the rotation first. However, both files t1.pdb and t2.pdb had the torsion changed 90 degrees from the original 1gcn structure. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On May 1, 2018, at 9:57 PM, Rodrigo Galindo-Murillo <rodrigogalindo@gmail.com> wrote:

Hello!

I need to do a dihedral scan around the phi/psi angles of alanine dipeptide and to create the input files to later do single point calculations I am using the cmd script:

open ../scan.pdb rotation 0 @/serialNumber=7 @/serialNumber=9 rotation 0 180 write format pdb #0 test.pdb

I need to use atom serial numbers since the idea is later do the scan with non-canonical peptides that will not work with the native phi/psi descriptions.

The script is not modifying any angle but I can see that is generating test.pdb correctly. Could you please orient me if this is the correct set of instructions?

Thank you!

Rodrigo.