Thank you for all reply! You guys are really helpful! I appreciate it! Bing ________________________________________ From: Oliver Clarke [oc2...@columbia.edu] Sent: Monday, August 11, 2014 4:21 PM To: CCP4BB@JISCMAIL.AC.UK; Wang, Bing Subject: Re: Add water in the symmetry center?
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 <bingw...@ou.edu> 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 >
