[Chimera-users] Align the molecule

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 8 09:28:41 PST 2010

Hi S,
As described in this recent post,

you can use the "align" command to put one or more atoms in front and  
one or more atoms in back (aligns them along the Z axis in the center  
of the screen), then use "turn" to rotate the alignment to other axes.

For example, including 3 different possibilities for "align":

open 1gcn
align :1.a :29.a
   ( - OR - )
align :1.a at n :29.a at c
   ( - OR - )
align :1.a at n,ca,c :29.a at n,ca,c
turn y 90

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 8, 2010, at 8:52 AM, snoze pa wrote:

> Dear Chimera Users,
> I am wondering if it is possible to align the molecule along the X-Y
> or Z axis. I want to place the molecule, along a line joining N to C
> terminal line. Idea is to place a molecule along this line(N to C
> line) which is X or Y or Z axis.
> Thank you,
> S

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