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Superimposing Molecules

Water Positions

Placing waters in a crystal structure is a critical task - waters can easily be used to suppress noise in the data and hence introduce Model Bias. In the presence of two or more independent structures of the same molecule, however, waters that are in the same position in all molecules are most likely to be correctly placed. Furthermore, especially if the crystallisation conditions are different, matching waters may be of biological relevance.

There are many ways to obtain such a list. The first step is to superpose all structures relevant structures. The following programs can produce a list of matching waters:

  • lsqman. The command WAters prints the desired list.
  • RasMol. The powerful selection rules from RasMol can be applied with the command
 select (water and *:W) and within(0.7,(water and *:X)). 

This selects all waters of chain 'W' (which is supposed to contain the water molecules of the first structure) and all waters from chain 'X', which is supposed to conatin the water molecules of the second structure, but only those within 0.7A distance to any of the other atoms.

  • People from the small molecule world can also use the ENVI command from XP.