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Hi Robbie, I updated my stripper program to remove all atoms with occ<0.00 instead of > 0.00 > - I used to do it in the past in phenix.model_vs_data but then I found it too boring since it was silently swallowing the problem cases -:) so I reverted it back to the "naive mode" when it takes what's in PDB as "God given" and computes the stats using it. This in turn points out problem cases, which is instructive, and which one can take care of on a second walk-through. - Also, you will be missing things like this: > http://www.rcsb.org/pdb/files/3otj.pdb http://www.rcsb.org/pdb/files/3kcj.pdb (.. and so on, I have a full list) where, I guess, "D" with negative occupancy actually means H -:) All the best! Pavel.