This command reads a PDB and outputs a file called with the name given for the output-file parameter (NEVER GIVE THE SAME NAME OF THE PDB YOU ARE READING OR YOU WILL OVERWRITE IT) in which the crystallographic water bridges (those waters making 2 or more bonds to the protein) are printed. The minimal configuration file for CrystalWaters:
command=CrystalWaters pdb=CW.pdb pdbWaters=true
It can be run from the command line
foldx4 --command=CrystalWaters --pdb=CW.pdb --pdbWaters=true
FoldX uses output-file as a tag to label different outputs from different commands in batch runs. After running CrystalWaters you'll get one or two files to look at. Given output-file="TAG" the output files are:
- TAG_CW.fxout -> Crystal waters prediction, if no crystal water is predicted the following file won't be created
- Compare_water.txt -> a comparison between the predicted and crystal water bridges is made. In this file we use FAILED when the predicted water bridge does not have a crystal counterpart (we do not consider neighbour crystal units) and PREDICTED when the distance is less than 1 Å (the first number is the distance). At the end of the file the ratio between predicted water bridges with a counterpart in the X-ray and total number of X-ray water bridges is shown.
If you don't set output-file, TAG will be the pdbId of the first pdb on the batch.