Phasing with HKL-3000
There is already a guide on how to solve structure by S-SAD phasing using Shelx in hkl2map. The same can also be achieved directly in HKL-3000. To do that, go to the Structure tab. If no sequence is associated with your project, an error will pop up, asking you to edit your project. Note how the scaled data is now part of the project. Saving the project at this point can't hurt.
Now click on the Data Analysis button at the bottom of the Data Analysis tab. The anomalous signal is strong if the curve is in the light area of the chart.
Click on the Find Sites tab to run ShelxD. ShelxD will stop as soon as a solution has been found (identified by virtue of high CC all and FOM relative to the rest).
You can view the sites, but you might as well continue straight to the Phase tab. Phasing is done with MLphare. First, disambiguate the handedness of the solution. Click Check Hand. One solution will have much better statistics. This is automatically used.
Then click Phase. This will be done quickly. I didn't take a picture.
The next step is chain tracing and building. arp/warp is used by HKL-3000. The advantage over ShelxE is that the sequence is threaded onto the C-alpha chain. The result is shown at the bottom. Even waters have been placed already.