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I shall be grateful THANKS & REGARDS! Tallat Hussain Ghazi IT Manager / Head of Web & Graphics Depts. ITSS (Pvt) Ltd. Email: tal...@itssols.com Website: www.itssols.com Mob: +92 (0)323 9900002 Tel: +92 (0)42 5694723-25 Fax: +92 (0)42 5694727 -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keitaro Yamashita Sent: Monday, April 16, 2012 7:09 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] bulk solvent treatment inside protein cavities 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_l > inux.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 > > > >
