Mohamed,
you seem to think that xia2 and XDS are at the same level in the hierarchy of crystallographic programs. This is not so. Rather, xia2 is what I would call "a layered product": it is basically a script that runs MOSFLM or XDS - that choice is up to the user.
What you should do depends on whether you chose the MOSFLM or XDS way of running xia2. I would propose:
- if you ran MOSFLM (from xia2) you have a number of (multi-record) MTZ files. You should then convert, using pointless, the XDS_ASCII.HKL files that you got from "manual" processing to (multi-record) MTZ files. Then scale and merge everything with aimless.
- if you ran XDS (from xia2) then you should scale and merge, using XSCALE, all XDS_ASCII.HKL files. Alternatively (and as a matter of personal judgement), you could use pointless and aimless.
Hope this helps,
Kay
P.S. users should realize that xia2 is not an alternative to the XDS and MOSFLM programs, and document this in their references, and their PDB depositions ... AFAIK the xia2 docs and output is clear about this.
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