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
