Phaser-2.1
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Thank you for downloading tutorial files for using Phaser-2.1 to solve
structures by molecular replacement.  These molecular replacement tutorials
will also work with the older Phaser-1.3.

Please follow the online tutorial which can be found at 
http://www-structmed.cimr.cam.ac.uk/phaser/tutorial/keyword_tutorial.html

Example 1: toxd
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First use coot to superimpose 1BIK.pdb on 1D0D_B.pdb, saving the new
coordinates in 1BIK_on_1D0D.pdb.

>source AUTO_toxd1.com
>source AUTO_toxd2.com

This solves the structure of toxd automatically, using either one 
structure or an ensemble of two structures for the model.  Note that,
when you use an ensemble, the members of the ensemble have to be superimposed
on each other into a common orientation.

Example 2: beta-blip
--------------------
>source AUTO_beta_blip.com

This solves the structure of the beta-lactamase/beta-lactamase-inhibitor
(BETA/BLIP) complex. BETA is 62% of the scattering and is easy to locate,
but BLIP is much harder to locate. Phaser uses the information from the
solution of BETA to help find BLIP.

Example 3: individual steps
---------------------------
>source AUTO_beta.com
>source ROT_blip_fixbeta.com
>source TRA_blip_fixbeta.com

Here the search for the BLIP component is broken into separate rotation
and translation runs.

Documentation
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Further examples using the beta-blip test data can be found in the phaser
documentation
http://www-structmed.cimr.cam.ac.uk/phaser/documentation/phaser-2.1_key.html
