On 16 Apr 2012, at 17:14, Keitaro Yamashita wrote: > 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.
ok > > >> 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? There could be some differences, as I said FC_ALL maximum likelihood scaled (they are used for map calculation) and FC_ALL_LS least-squares scaled (it is used for Rfactor calculations) > > I found somewhat large difference between FC_ALL_LS map and FC_ALL > map in Se position. Without data I could not say what might be going on. > 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 >> >> >> >> 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
