Re: [ccp4bb] Water molecules after refinement
This may be a useful paper to read, although it is a bit dated: Acta Cryst. (1999). D55, 479-483 How many water molecules can be detected by protein crystallography? In general, 3 A resolution is beyond where you can reliably add waters (I start adding them only at 2.7-2.8 A resolution or better). If you do want to add waters, make sure they make sense (H-bonding/distance) and do not have positive Fo-Fc density after refinement, in which case they could be metal ions. If after refinement the (2Fo-Fc) density disappears then whatever you thought was there isn't. best, bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of jeorgemarley thomas [kirtswab...@gmail.com] Sent: Wednesday, November 19, 2014 6:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Water molecules after refinement Dear All, I am sorry to ask this simple question, but I really need suggestions for this. As the refinement has been done at 3.0 Angstrom after refinement the water molecules were added by using find waters in coot. After adding water refinement was done using Refmac 05. Now when I look on the added water molecules some has density around it and some does not (even no red density around it). Should I remove later water molecules. and again do the refinement ? Please give some explanation also for this. as the R free and R meas has reduced to some extent, also the r m s d contour of map level was kept at 1.09 after refinement. I welcome your suggestions, thanks in advance. Regards Jeorge
Re: [ccp4bb] Water molecules after refinement
Dear Jeorge, as you add water molecules to a model, the R _and_ Rfree are bound to drop. It is important to do it the other way round: let coot add waters, then check the added waters in coot if they make chemically sense, then run refmac5. Don't trust automatic procedures more than your chemical education, no matter how fancy. At 3A I would be careful adding any waters at all, you might just fit noise. Best, Tim On 11/19/2014 07:33 AM, jeorgemarley thomas wrote: Dear All, I am sorry to ask this simple question, but I really need suggestions for this. As the refinement has been done at 3.0 Angstrom after refinement the water molecules were added by using find waters in coot. After adding water refinement was done using Refmac 05. Now when I look on the added water molecules some has density around it and some does not (even no red density around it). Should I remove later water molecules. and again do the refinement ? Please give some explanation also for this. as the R free and R meas has reduced to some extent, also the r m s d contour of map level was kept at 1.09 after refinement. I welcome your suggestions, thanks in advance. Regards Jeorge -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
Re: [ccp4bb] Water molecules after refinement
Dear Jeorge are the water molecules without electron density properly coordinated? These could be ghosts... Additionally, did you solve the structure by molecular replacement? If so, in your search model, do you see these water molecules at the same / nearby location? Again, those could be model bias. Finally, depending on your resolution, you can expect a certain amount of water molecule (depends on other factors, obviously). If you find 'too many' (difficult to define 'too many'), it might be one indication that you are over-refining things. I know I did not answer your question, but hope this could help. Others will have better comments I guess. Cheers, Leo On 19 Nov 2014, at 07:33, jeorgemarley thomas kirtswab...@gmail.com wrote: Dear All, I am sorry to ask this simple question, but I really need suggestions for this. As the refinement has been done at 3.0 Angstrom after refinement the water molecules were added by using find waters in coot. After adding water refinement was done using Refmac 05. Now when I look on the added water molecules some has density around it and some does not (even no red density around it). Should I remove later water molecules. and again do the refinement ? Please give some explanation also for this. as the R free and R meas has reduced to some extent, also the r m s d contour of map level was kept at 1.09 after refinement. I welcome your suggestions, thanks in advance. Regards Jeorge
