[Chimera-users] generate helical symmetry mates around an axis

[Elaine Meng]

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 at 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