[Chimera-users] Align the molecule

[Elaine Meng]

Hi S,
As described in this recent post,
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-February/004768.html 
 >

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
rlabel
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
focus

I hope this helps,
Elaine
-----
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