Dear Anja, every integration software determines and most likely also prints the orientation matrix of the crystal's unit cell w.r.t. the laboratory coordinate system. With XDS, this matrix can be found in GXPARM.XDS, with mosflm you entered that matrix' name when you refined the cell parameters.
For image 0 this is the orientation matrix you can apply to your coordinates (there is probably also a way in pymol to apply a rotation matrix to what you see on the screen), for any other image you have to apply a rotation matrix for the rotation angle and axis to that orientation matrix first. See e.g. http://en.wikipedia.org/wiki/Rotation_matrix ("Rotation matrix given an axis and an angle") for how to calculate the such a rotation matrix. There are two tricky bits: 1) Figuer out how the laboratoy coordinate system is oriented, because this is software dependent. For XDS that's particularly easy and discribed thoroughly on http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/coordinate_systems.html For other processing programs it may be as easy, I just happen not to know where this is documented. 2) Figure out what coordinate system pymol lives in. A quick search on the pymol wiki (http://www.pymolwiki.org) did not reveal this to me. Tim On Wed, Jul 07, 2010 at 05:22:23PM +0200, Anja Pomowski wrote: > Hi there, > > we were taking UV/ vis spectra of a protein crystal that show > different features depending on the crystal orientation in the beam. > The question is now how to correlate the UV/ vis spectra with the solved > structure. We know that it has a special feature at e.g. image 1 (0°). So > how can we get the orientation of the molecule in pymol so that it > corresponds to its orientation in the crystal at that exact image? > > Thanks a lot, > > Anja > > > > > > Anja Pomowski > > Universität Freiburg > Institut f. Organ. Chemie und Biochemie > AK Prof. Einsle > Albertstr. 21 > 79104 Freiburg > > Tel. 0761 2036088 > Fax. 0761 2036161 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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