Best practices in handling crystal waters?

[jchodera]

Do we have an established best practice on how crystallographic waters should be handled?

One possible practice (from @bobym) is to keep the following kinds of waters:

• Waters within 3A from any HETATM groups (reference ligand, ions, cofactors, etc.)
• Bridging waters (waters that have two or more hydrogen bonds to non-waters), which could include structural waters

[jchodera]

We currently say this:

[jchodera]

We should also revise the checklist to be more explicit.

[davidlmobley]

To my knowledge there is no literature yet which has studied what are the best practices here. The practice you recommend seems reasonable.