Processing and scaling one sweep
xia2 -2d -image /the/data/are/here_001.img
(or using XDS / XSCALE)
xia2 -3d -image /the/data/are/here_001.img
The same but for multiple sweeps for the project
xia2 (-2d|-3d) /the/data/are/here/
where (this|that) means this or that.
If you have only one wavelength of data recorded in there but want to have anomalous pairs separated, tell the program there is a heavy atom in there. You can lie!
xia2 -atom X -3d /etc
Now, sometimes when you are starting up you know the cell and symmetry for the project. Why not share that?
xia2 -cell a,b,c,alpha,beta,gamma -spacegroup PXXX -2d /etc
Some more fiddly cases will need to be indexed from all of the available images, so use the 3DII pipeline in place of 3D:
xia2 -3dii /etc
- this is particularly useful when combined with the cell and symmetry input. Finally, if you want to run this in background, do
xia2 /etc > xia2.log 2>&1 &
(bash syntax) which will run it in background so as you can close the shell or log out.
For more complex usage of xia2, you get into the realms of needing to compose an input file. This is really not all that hard, and is actually the first thing which xia2 did in the examples above (go look for automatic.xinfo). The advantages of composing your own input file are that you can set out exactly what you want to happen, without the program guessing. The disadvantages are that you need to get the syntax right and understand what you can do, hence this documentation!
The basic structure of the input file is as follows:
BEGIN PROJECT PNAME
BEGIN CRYSTAL XNAME
BEGIN WAVELENGTH WNAME
END WAVELENGTH WNAME
BEGIN SWEEP SNAME
WAVELENGTH WNAME
DIRECTORY …
IMAGE …
END SWEEP SNAME
END CRYSTAL XNAME
END PROJECT PNAME
Now there’s lots that can be added to this - I will go through this all one chunk at a time.
USER_CELL 150 170 270 90 100 90
USER_SPACEGROUP C2