Dear All, Using the 'Find waters' dialog with coot v.0.7-pre-1 (revision 4455) Linux-i686-ubuntu-10.04.4-python-gtk2, appears to be sensitive to the location of the model. I have a model that is translated by 2 unit cells along Z. When I use 'find waters' with that model location, the console output is :
----------------------------------------------------------------------------------------------------------------- finding peaks above 1.2 sigma Protein centre at: xyz = ( 17.12, -10.44, 212.8) using sigma cut off 1.2 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.42901 INFO:: Using density cut-off: 0.514812 (1.2 sigma) (mean -0.0512968 stdev: 0.154434) INFO:: Using water to protein distance limits: 2 6 Finding clusters...done ------------------------------------------------------------- INFO:: found 0 waters in water fitting Done - back from lig.water_fit() ----------------------------------------------------------------------------------------------------------------- If I translate with model (with SYMGEN X,Y,Z-2 in pdbset) and re-run it : ----------------------------------------------------------------------------------------------------------------- finding peaks above 1.2 sigma Protein centre at: xyz = ( 36.11, -10.44, 26.5) using sigma cut off 1.2 Calling lig.water_fit() INFO:: find_clusters map_rms is 0.441313 INFO:: Using density cut-off: 0.529576 (1.2 sigma) (mean -0.0575211 stdev: 0.114877) INFO:: Using water to protein distance limits: 2.4 3.2 Finding clusters...done ------------------------------------------------------------- INFO:: found 23 waters in water fitting Done - back from lig.water_fit() DEBUG:: new_waters_mol_flag: 1 Symmetry available for this molecule ----------------------------------------------------------------------------------------------------------------- The problem is that even after the translation, some putative waters appear to still escape detection. Can anyone confirm that the problem exists, or it is me doing something wrong ? All the best, Nicholas
