Dear Garib, Thank you very much for your quick reply.
I tried mskout option and the output looked almost the same as the map generated by FC_ALL - FC. By the way, when mskout option is specified, refmac stops before CGMAT cycles. Is there any way to do refinement with mskout option? > I have not tried but if you can use vector difference map then it should be: > FMASK = FC_ALL_LS - FC What is FC_ALL in the new version? Thanks, Keitaro 2012/4/16 Garib N Murshudov <ga...@mrc-lmb.cam.ac.uk>: > A follow up: > > In the new version there is FC_ALL_LS, PHIC_ALL_LS > > That should be FC_ALL_LS = FC + FMASK. > > I have not tried but if you can use vector difference map then it should be: > FMASK = FC_ALL_LS - FC > > But it is after scaling. If you write out mask map then it is just 0 1 map > (0 inside protein and 1 outside), except values are not 0 1 but 0 and some > constant > > > > Regards > Garib > > > On 16 Apr 2012, at 15:09, Keitaro Yamashita wrote: > > 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 > > > > > > > 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 > > > >
