Dear Garib, I think it is better if refmac outputs final solvent mask when mskout specified. If one just wanted to calculate the mask, NCYC 0 should be specified.
I hope my suggestion would be accepted, but I'm not in a hurry. > FC_ALL is ML scaled FC+FMASK > > Sometime it may be different from least-squares scaled FC+FMASK For what purpose is FC_ALL_LS written? Can I check something by comparing FC_ALLto FC_ALL_LS? I found somewhat large difference between FC_ALL_LS map and FC_ALL map in Se position. I used SAD function. What does it mean? Cheers, Keitaro 2012/4/17 Garib N Murshudov <ga...@mrc-lmb.cam.ac.uk>: > 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 > > > >
