Hi Rajesh, If you're seeing a lot of extra density coming up in the map in regions where you previously added waters, is it possible that this extra density corresponds to a part of your protein that you previously thought was disordered and is thus missing from the current model? At this resolution you wouldn't expect to see many waters. Also, to the best of my knowledge, the relative weighting of the X-ray and geometry terms in BUSTER is set by the program so as to produce a rmsd in bond lengths equal to a target value. The default value of this is 0.01 Ang (I think) but you can change this using the -r option on the command line. Using a lower value will reduce the weight on the X-ray term and may lower the R/R-free gap. Best wishes, Joe
> > > Dear All, > I have a 3.3 A data for a protein whose SG is P6522. Model used was wild > type structure of same protein at 2.3 A. After molecular replacement, > first three rounds of refinement the R/Rf was 26/32.8, 27.1/31.72 % and > 7.35/30.88 % respectively.In the fourth round I refined with TLS and NCS > abd added water and the R/Rf dropped to 19.34/26.46. It has almost 7% > difference. I also see lot of unanswerable density in the map where lot of > waters were placed. Model fits to the map like a low resolution data with > most of side chains don't have best density. > I was not expecting such a sudden drop in the R/Rfree and a difference is > 7.2%. I am wondering if I am in right direction. I am not sure if this > usual for 3.3A data or in general any data if we consider the difference. > I appreciate your valuable suggestions. > ThanksRaj > >
