Hi Sadeem, Axis objects from the "define" command cannot be used as axis specifications for the sym command. See the "sym" command documentation for how to specify axes: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html> "Specify axis of symmetry (default z), where the axis value can be: • x - X-axis • y - Y-axis • z - Z-axis • x,y,z (three values separated by commas only) - an arbitrary vector in the reference coordinate system • an atom-spec of exactly two atoms (not necessarily bonded or in the same model) or one bond. A bond can only be specified by selecting it and using the word selected, sel, or picked; any atoms also selected at the time will be ignored." I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 10, 2020, at 12:18 PM, sadeem ahmad <sadeemahmad@gmail.com> wrote:
Hi all, I am trying to generate a helical trimer from the monomer pdb around a central double-stranded RNA. The rise and twist are 46 A and 74.0 deg respectively. I opened my monomer pdb in chimera (Screenshot-0) and used the following command to generate an axis around the central RNA double helix:
define axis #0:.X,.Y
where X and Y are the chain IDs for the 2 RNA strands
This command helped me generate an axis named a1 along the RNA duplex (Screenshot-1). Now I want to generate a helical trimer along the RNA duplex with rise=46A and twist=74deg. For this I used the command:
sym #0 group H,46,74,3 axis a1
However, it is not placing the symmetric copies around axis a1 but around a distant axis (Screenshot-2). I am not sure how to generate the helical trimer along the a1 axis. Any help in this regard would be appreciated. Thanks.
-Sadeem