Build water into cryo-EM map using phenix.douse

phenix.douse is a tool to build water into cryo-EM maps.


Command line, GUI.

Required inputs

Atomic model (PDB or mmCIF format) and map (MRC format).

Optional inputs

mode = whole or per_chain: work on the whole model or per chain. Working on the whole model may require a lot of memory.

sphericity_filter = True: use peak sphericity criteria. Disable to add more water.

keep_input_water = False: keep or remove existing water.

dist_min = 2.0: minimal peak-peak or peak-atom distance. Decrease to add more water.

dist_max = 3.2: maximal peak-peak or peak-atom distance. Increase to add more water.

step = 0.3: map re-sampling step.

map_threshold = 1.0: scale factor for automatically determined map threshold. Decrease to add more water.

scc05 = 0.97 and scc1 = 0.9: sphericity characteristics. Decrease to add more water.


P1 symmetry is the only supported symmetry.


Macromolecular part of the atomic model is as compltete as possible (no missing chains or other unmodelled parts present).

Map resolution is sufficently high to expect water oxygens be visible in the map.


phenix.douse model.pdb map.mrc

More information


Pavel Afonine (