I think I've answered my own question:
https://sourceforge.net/p/pymol/mailman/message/27824450/

Thanks a lot Jared!

On 1 Sep 2016, at 9:47 AM, #YEO JINGJIE# 
<jy...@e.ntu.edu.sg<mailto:jy...@e.ntu.edu.sg>> wrote:

Hi Jared,

Thank you very much for your information. However, it seems that orient only 
changes the viewpoint, may I know whether it would possible to change the 
coordinates accordingly and save it into a pdb?

Best Regards,
Jingjie

On 31 Aug 2016, at 10:16 PM, Sampson, Jared M. 
<jms2...@cumc.columbia.edu<mailto:jms2...@cumc.columbia.edu>> wrote:

Hi Jingjie -

The `orient<http://www.pymolwiki.org/index.php/Orient>` command does this, 
although you can't specify which axis.  However, when combined with 
`turn<http://www.pymolwiki.org/index.php/Turn>` or 
`rotate<http://www.pymolwiki.org/index.php/Rotate>`, you can get the molecule 
aligned in whichever orientation you prefer.  E.g:

orient myprotein
turn x, 90
turn y, -90

Hope that helps.

Cheers,
Jared


On Aug 31, 2016, at 6:10 PM, #YEO JINGJIE# 
<jy...@e.ntu.edu.sg<mailto:jy...@e.ntu.edu.sg>> wrote:

Dear Users,

May I know whether there are any methods in pymol to rotate a protein such that 
it's longest principal axis is in a particular direction, for instance aligned 
to the x-axis?

Best Regards,
Jingjie
**Disclaimer** The sender of this email does not represent Nanyang 
Technological University and this email does not express the views or opinions 
of the University.

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