Dear Michael, did you also check you are using the same binary? You might be using findwaters from the CCP4 tree on the command line and from within the coot-tree when using coot, in case you installed coot separately on top of ccp4 (or maybe phenix?).
Best, Tim On 03/11/2014 08:14 AM, Michael Engel wrote: > 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 > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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