Thomas Schneider's SHELX FAQs website has most of the typical problems that you'll run into, so you're encouraged to go there if you can't find what you need here! Or you can e-mail your question to Chris Waddling.
1. Now that I have updated the path in my .cshrc file and can run Shelx, what do I need to do first? - Set up .ins and .hkl files in Shelxpro, including Rfree flags.
2. Will Shelxl work right away after setting up the .hkl and .ins files?
3. I already have alternate conformations in my .pdb. Will they be ok in Shelx?
4. How do I set up parameters for things Shelx doesn't recognize?
5. Running Shelx at UCSF
6. Generating maps for O
7. Getting alternate conformations to show up in O
8. Hydrogen atoms in O
9. Making changes in O and then going back to Shelx for more - the tricky part!
10. Restraining occupancies of all atoms in partially occupied ions or molecules - FVAR
11. Dimers - Thanks C.R.
12. Shelxl crashes when I have more than 150000 unique data - Thanks L.R. & C.F.
13. The final step: getting esds, etc. using L.S. - why doesn't it work? - Thanks K.R.