Integration with Denzo

After having obtained the refined alignment parameters, you need to edit the input file for the DENZO integration run. Get a sample input file with
`$ copy $p:[denzo.example]integ.dat *`
or just click here for one. Edit the file with
`$ edit /tpu integ.dat`
You'll need to set the `format` again (`mar 18cm` or `mar 30cm`), as well as the mosaicity, spacegroup, image file names etc.
A bit further down you'll need to paste in the file with the "Current parameter values" which you hopefully saved at the end of your auto-indexing session. Click here for a sample.
There are endless variations on the refinement protocol for each image as it is integrated. Basically, the loop between `[refinement starts here]` and `end of pack` will be executed for every image (see `sector` command above) and a .pro or .yrk file will be created from every image.
When you're done editing, submit the integration run to a batch queue. You can do this with the file denzo.com, don't forget to edit the
`$ set def` command in that file. Then
`$ submit /log=[] /noprint /noti denzo.com`

The next step is the scaling and merging of all data from the individual .pro files generated by DENZO. Also, partials can be added at this time.
One program that does this is SCALEPACK, part of the HKL package.
Alternatively, you can use the CCP4 program suite, in which case you need to run your integration with `film york output file` (see file integ.dat). Click here for a sample input file.