[Chimera-users] Align the molecule

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 8 09:34:44 PST 2010

I forgot to say: another possibility instead of using "align" is to  
display the helix axis as a cylinder with the "define" command or the  
"Axes/Planes/Centroids" tool and then orient the axis by hand.  It may  
be easiest to do this along Z so you are looking at the end of the  
cylinder, then use "turn" as before to align along different axes.



open 1gcn
define axis perHelix true


On Feb 8, 2010, at 9:28 AM, Elaine Meng wrote:

> 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
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