[Chimera-users] Question regarding rotating dihedrals

[Elaine Meng]

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 at 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.