This means that the unit cell in the MTZ file obtained from the density is non-orthogonal, i.e. the angles are not all 90 degrees.  Although in principle we could have made it possible to use non-orthogonal unit cells, it would make things more difficult for us and, since the density has to be cut out and put in a new unit cell with lots of space around it anyway, there's no reason not to choose an orthogonal unit cell.

If you use Kevin Cowtan's cmapcut to cut out the density for MR, it will choose an orthogonal unit cell by default.

This reminds me that I must update our web page on using electron density as a model!  Before Kevin's nice cmapcut program (and Tom Terwilliger's equally nice phenix.cut_out_density procedure) it was a laborious process that required a very long explanation.

Best wishes,

Randy Read

On 17 Jan 2013, at 03:20, Wei Feng wrote:

Dear all, 
When I used PHASER to do a molecular replacement and define ensemble via map (mtz file), the program stoped very soon. 
The log file showed that "Unit Cell of Ensemble must be orthogonal".
I tried many ways to generate the map file, but the results are the same.
Can anyone help me to solve this problem?
Thanks a lot!
Wei



------
Randy J. Read
Department of Haematology, University of Cambridge
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