Build water into cryo-EM map using phenix.douse

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

Availability

Command line, GUI.

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

resolution is required if cc_mask_filter is set to True.

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.

scc = 0.5: map peak sphericity characteristic. Decrease 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_scale = 0.5: map threshold for peak selection = (mean map value at atom centers) * map_threshold_scale Decrease to add more water.

cc_mask_filter = True: Reject water with CC_mask < cc_mask_filter_threshold.

cc_mask_filter_threshold = 0.5: CC_mask threshold for rejecting 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 resolution=2.5

resolution is required if cc_mask_filter is set to True.