Dear Ketaro At the moment mskout option is a signal that the program should stop. Obviously I can add an option to continue. However if you have mskout option it is likely that you want to check what is going on with the mask. If you want to compare starting and final mask then you could run refmac with mskout in the beginning and after refinement.
If you need it urgently then I can add continuation of refinement with mskout option. FC_ALL is ML scaled FC+FMASK Sometime it may be different from least-squares scaled FC+FMASK regards Garib On 16 Apr 2012, at 16:01, Keitaro Yamashita wrote: > 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 >> >> >> >> 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
