Dear All,

Thanks for all the suggestion. Data is anisotropic. Since anisotropic correction with the UCLA server didnt give any good  Molprobity scores and didnt reduce the R/Rfree at 2.1A, I am using ~3.3A data for further refinement. 

Using Tom's suggestion of target restrains reduced the gap brtween R/Rfee to with in 5%.  I haven't tried Pavel' suggestion but when I do I will post the results.

I used a 2.3 A MR model as target to get R/Rfree 0.2209/0.2597. When I used coot real space refine zone to fix few molprobity outliers, most of the favored residues become outliers. Almost all residues changed to become outliers. I am wondering why all the residues are moving from favored to outlier regions after restrained refinement. I thought all the residues would be fixed (fit) to the map and  wouldn't change during the coot exercise, and this is what I see in the 2.3 A target/model structure ( with R/Rfree 0.1693/0.1961). 

 I don't know if is this common  for a low resolution or I didn't understand this whole thing of refinement correctly.

Thanks for all the help,

Regards,
Raj

> Date: Sun, 4 Mar 2012 21:02:51 +0000
> From: [log in to unmask]
> Subject: Re: [ccp4bb] sudden drop in R/Rfree
> To: [log in to unmask]
>
> Presumably your data is quite anisotropic, and low resolution, so it is
> quite likely that a TLS model will give much better description of the B
> factors than more classical refinement.
>
> Modelling solvent at that resolotion will be tricky of course.
> Elesnor
>
>
>
> On Mar 4 2012, Joseph Cockburn wrote:
>
> >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
> >>
> >>
> >
>
> --
> Professor Eleanor Dodson
> YSNL, Dept of Chemistry
> University of York
> Heslington YO10 5YW
> tel: 00 44 1904 328259
> Fax: 00 44 1904 328266