Dear Garib, Is there REFMAC option to output solvent mask information (e.g. Fmask and PHImask in mtz to check with Coot)?
I tried to generate it by subtracting (FC, PHIC) from (FC_ALL,PHIC_ALL). But I'm not sure that FC_ALL = FC + FMASK is correct or not. Keitaro 2012/4/16 Garib N Murshudov <ga...@mrc-lmb.cam.ac.uk>: > Dear Allister > > Could you please update refmac version. In the version you it seems that > bulk solvent mask calculation has some problems. New version (at the moment) > can be downloaded from this site: > > http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.7_linux.tar.gz > > There is a mac version also. > > > regards > Garib > > > On 16 Apr 2012, at 11:37, Allister Crow wrote: > > > Board members, > > I have a couple of questions regarding how to improve the solvent model as > applied to solvent-filled cavities inside proteins. > > I am currently nearing the end of refinement of a protein structure at 2.8 A > resolution. I recently switched Refmac versions, upon doing this I noticed > a modest improvement in R factors, but I also notice some new features in > the difference maps. These features don't show up in the sigma-weighted > 2Fo-Fc maps and are unlikely to be 'ligands' of any form. In fact, I > suspect that the appearance of these features (which are all located in > solvent channels within cavities inside the protein) are probably due to > some difference in how the bulk solvent contribution has been applied. > > I've attached a picture of one such feature showing the difference between > Refmac 5.5 and 5.6. (Both difference maps are contoured at 3 sigma- both > using the same model and refinement parameters). > > My questions are therefore: > > 1) has something substantial changed in the bulk solvent treatment between > Refmac versions 5.5 and 5.6? > > 2) How can I go about changing the bulk solvent treatment to better account > for solvent contribution inside the protein cavities? > > Best wishes, and thanks in advance for all your help, > > - Allister Crow > > > <bulk_solvent_inside_cavities.png> > > > > Dr Garib N Murshudov > Group Leader, MRC Laboratory of Molecular Biology > Hills Road > Cambridge > CB2 0QH UK > Email: ga...@mrc-lmb.cam.ac.uk > Web http://www.mrc-lmb.cam.ac.uk > > > >
