[Chimera-users] Aligning on crystal axis

Tom Goddard goddard at sonic.net
Tue Jun 2 10:47:09 PDT 2015

Hi Mohamed,

  When you first start Chimera and open a PDB x-ray model or density map you will be looking exactly along the z axis which is perpendicular to the crystal unit cel ab face.  The “reset” command (menu Favorites / Command-Line) will reset to this position if you rotate the models.  If the cell angles were 90 degrees you could rotate 90 degrees about y with command "turn y 90” to view along the x axis (bc face).  But I guess you are interested in the case where the cell angles are not 90 degrees.  There is no Chimera command to view perpendicular to the ac and bc faces in that case.  But if you have a PDB model you could show the unit cell outline box (menu Tools / Higher-Order Structure / Unit Cell) and you could use orthographic projection ("set projection orthographic”) then hand rotate so the unit cell outline front and back ac faces exactly overlap each other.


> On Jun 2, 2015, at 9:18 AM, Mohamed Noor  wrote:
> Hello.
> Is there any easy way to align the view along the crystal axes, such as the ab, ac and bc faces separately?
> Thanks.
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