Hi, I can't reproduce the results I get by using find waters from within coot when running findwaters on the command line on the same pdb/mtz. I have double checked all the command line switches are the same and compared the output in the log files. Nothing obviously different but I am getting nearly 3x as many waters when running findwaters externally compared to starting it from the GUI, so as if the sigma was on a different scale. Although the water to protein distance limits are reported to be same, I couldn't find the command line switch to change them from their default values.
System is coot 0.7.2 on ubuntu 12.04 LTS. Any help would be greatly appreciated. Cheers, Michael
