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Dear Bing, My best guess is that these are artefacts due to the increased noise level at special positions (in your case a sixfold increase - see for example: http://scripts.iucr.org/cgi-bin/paper?S0365110X66000264). I agree with your assessment that it is best to leave such peaks unmodelled unless their interpretation makes chemical sense. Best, Oliver. On Mon, 11 Aug 2014 16:47:05 +0000, Wang, Bing <[log in to unmask]> wrote: >Hi guys, > >Recently I am working on a structure with a P6 space group and a nice resolution. The model I used is perfect to fit the electron density. However, I found a couple of weird water molecules which are located in the symmetry center or the middle of two molecules (Please check the attachment). I am wondering how to define these "fake" waters and should I add water here or not. Reasons? > >For my opinion, waters in the structure that we can see should have some ways to fix them, otherwise they will flow in the channel and can't be seen in the structure. I prefer to add water in the postion2 since the Arg residue could fix a water molecule there, but for others, I could not find any reasons to add water since there are no ways to fix these water molecules. Is it correct or not? > >Thank you! > >Bing >