Hi Jerry,
If you wanted the mathematically exact axis, you _should_ be able to
just make two pseudoatoms, position them at the proper position at the
end of your axis and then use the orient command:
pseudoatom axisMin, pos=[x1, y1, z1]
pseudoatom axisMax, pos=[x2, y2, z2]
orient axis*
But, there is a bug with 'orient' on pseudoatoms: it's orienting the
pseudoatoms along their 2nd principal axis, not the first. So, after
you type those three command, follow up with:
turn z, 90
and that should do it.
Hope this helps,
-- Jason
On Tue, Sep 7, 2010 at 1:37 PM, Sampson, Jared <[log in to unmask]> wrote:
> Hi Jerry,
>
> If your protein has an NCS symmetry axis parallel to a cell edge, you can try using the “orient” command.
>
> http://www.pymolwiki.org/index.php/Orient
>
> Best,
> Jared
>
>
> On 9/3/10 7:31 PM, "James Stroud" <[log in to unmask]> wrote:
>
> On Sep 3, 2010, at 4:03 PM, Jerry McCully wrote:
> It is a Pymol question. How can I set up the view through one axis of the unit cell?
>
> By eye. Use orthoscopic view to help. Show the unit cell as a guide:
>
> http://www.pymolwiki.org/index.php/Cell
>
> James
>
>
>
>
> --
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> New York, NY 10016
> (212) 263-7898
>
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--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
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