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Dear Jorge Since all my structures are below 1.7A ( between 1.2 to 1.7 A) I completely see what you see in my structures. I usually model these water molecules that are closer than 2.2 A to each other as two conformations of the same water and works pretty well for me. You can see a peanut shape map for these waters that are two conformations of the same water molecule. Soheila ________________________________ From: [EMAIL PROTECTED] on behalf of Jorge Iulek Sent: Wed 12/21/2005 5:17 AM To: [email protected] Subject: [ccp4bb]: refmac5 distance between water molecules *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** Dear all, I am refining a structure (almost 1100 residues in the au) at 1.6 A with refmac5. I could model a number of water molecules. At RCSB validation, I see several close contacts (in the same asymmetric unit) between water molecules (both at 1.00 occupancy). To investigate further, I used at refmac5: MONITOR MANY VDWR 1.5 In fact this lists several "bad" contacts including those reported by RCSB validation. Also, at refmac5 output, I see that 2.740 is considered to be the ideal distance between O's from water molecules, but it reports the several negative deviations (and several distance values below 2.2, 2.1 and even 2.0 A). I went to inspect maps and the model in coot. Interestingly, coot at its "check waters" tool does not list several of these "water close contacts" even when I ask it to list the ones lower than 2.2 A (does this distance work there also for between water molecules ? I could not find this at RTFM), but at measuring the distances there they are (even in the same au). In coot, I could see a number of cases where there is room for the molecule to go to "somewhere else" to avoid the bump at 2.2 A (distance used by RCSB). I thought this might be due to the fact that I am using higher weights (around 0.9) because of the resolution (and this gives me very good rms for bond angles and lengths). I lowered the weight to 0.3 and the problem persists (although a little less serious). I also made a test, put the same model into CNS and asked for only the water molecules to be refined. Then, no close contacts between water molecules at all ! I had never seen this problem (this is the first time I have a structure at 1.6 A). My questions are: a) How does refmac5 treat the distances between water molecules ? What is the weight imposed to this ? Has this something to do with the fact that the structure is 1.6 resolution and the weight is high ? If this is the case, how to use a high general weight (which gives better statistics at rms's and R factors) and not to have this problem with water molecules ? Has this something to do with the fact that I have a good number of waters (also because of the resolution) ? b) How to overcome this ? What I know is that arp might deal with this in real space, but there might still remain the fact thhat the new arp waters is further refined in refmac5 to distances lower than 2.2. Thanks, Jorge
