KappaCCD Program Flow (1.9)

This section describes the Single scan range Denzo-SMN GUI (version 1.9, using *.set files).
This version handles data collection scan ranges one at a time. If you have version 1.10 or higher, you need the description for the 1.10 version.

There are examples here showing how to process data with this version for single and multiple scan range data collections.

Single scan range data collections

using single scan range GUI A single scan data collection is often done at a zero detector swing angle ("straight on mode") at a short distance.

Description of action	Command	Intermediates
Data collection	Collect	s01f*.kcd (raw images)
Construct input file for Denzo	makeset s01f	s01f.set (Denzo GUI resource)
Start Denzo using s01f.set file	kc s01f	so1f*.x (Integrated Partials)
Execute Scalepack	(use GUI)	"compound".sca
Export to CIF file	cifin	import.cif

Multiple scan range data collections

using single scan range GUI All data collection sets have to be indexed and processed. Finally all *.x files are fed to scalepack using a script created by the mkscalein utility. Note that the total number of frames in version 1.9 is limited to 800.

Description of action	Command	Intermediates
Data collection	Collect	sf.kcd (raw images)
Construct input file for Denzo	makeset s01f makeset s02f makeset s03f	s01f.set (Denzo GUI resource) s02f.set s03f.set
Start Denzo using s01f.set file	kc s01f	sf.x (Integrated Partials)
Construct an input file for Scalepack	mkscalein	mkscale.in
Execute Scalepack	scalepack < mkscale.in	"compound".sca
Export to CIF file	cifin	import.cif

Remark:
In some cases indexing on separate scan ranges can take an alternative orientation, resulting in an inconsistent data set after merging all scan ranges.

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