I am not mistaken what went wrong in my case is that in resolve.mtz there are the columns FP and SIGFP which are not the experimental F anymore but they are modified ones (solvent flattened, ncs etc...). Clearly refmac5 uses them as Fo for refinement, refining Fc against Fc (an extreme case of over-refinement?), or in this case better say tautology.
stefano ---------------------------------------- > Date: Mon, 31 Mar 2008 16:50:13 +0100 > From: [EMAIL PROTECTED] > Subject: Re: [ccp4bb] too good R/Rfree with resolve > To: CCP4BB@JISCMAIL.AC.UK > > On Sun, Mar 30, 2008 at 07:08:14PM +0100, Partha Chakrabarti wrote: >> Is it by any chance that the FOMs were highly overestimated and that >> creates a problem with Maximum likelihood? That sort of reminds me of >> what I had heard for SHARP-solomon in a couple of instances.. > > The FOMs are never used in anything downstream from experimental > phasing and/or density modification - unless you calculate maps, but > even then you usually use some map coefficients directly. And to > describe the phase probability you should ideally use > Henrickson-Lattmann coefficients I guess. > > Anyway, if you want to use experimental phase information in > refinement (good idea), make sure to use the Henrickson-Lattmann > coefficients from the phasing program. The HLs after density > modification are usually over-optimisitic (at least for classical > density modification programs like SOLOMON or DM). > > I must admit I've never heard suspicions about the SHARP-solomon FOMs > before ... I could imagine people being generally supicious about FOMs > from any density modification program? I have very good experiences > using the HLs from SHARP afterwards during refinement. If you have > more details about this, I'd be very interested to hear! > > Cheers > > Clemens > > >> >> Any insight would be highly appreciated.. >> Regards, Partha >> >> >> On Fri, Mar 28, 2008 at 2:35 PM, Garib Murshudov wrote: >>> make sure that you are using the original observation (Fobs and >>> corresponding sigmas) not that produced by density modification (e.g. >>> solve resolve) programs. >>> >>> Garib >>> >>> >>> >>> On 28 Mar 2008, at 10:43, stefano ricagno wrote: >>> >>> > Dear CCP4bb readers, >>> > this is my problem: >>> > I solved a structure by MR: the solution was easily found (molrep, >>> > phaser and balbes found always the same one), density looked >>> > generally reasonable (however in several places it was dubious) but >>> > R/Rfree were stuck at 42/47%. >>> > Then I tried some density modifications, resolve worked >>> > spectacularly the density became wonderful and several parts which >>> > were not in the model appeared. >>> > So I finished to build the model and everything looked good. >>> > The problem is now for a structure at 2.8 Å resolution I have R/ >>> > Rfree of 8/9.5% respectively, which is clearly too good. Checking >>> > refmac log file it looked to me that refmac uses all the >>> > reflections in the .mtz file (that is as many reflections as before >>> > the resolve run). >>> > Ideas? >>> > >>> > thanks >>> > >>> > Stefano >>> > >>> > ps this is my last refmac: >>> > >>> > 2 mol in the AU, no NCS used, weighting term 0.01, no tls. >>> > >>> > Ncyc Rfact Rfree FOM -LL -LLfree rmsBOND >>> > zBOND rmsANGL zANGL rmsCHIRAL $$ >>> > $$ >>> > 0 0.0943 0.1051 0.937 102149. 5673.2 0.0070 >>> > 0.298 1.202 0.546 0.077 >>> > 1 0.0910 0.1024 0.940 101442. 5642.4 0.0058 >>> > 0.252 1.091 0.481 0.073 >>> > 2 0.0898 0.1019 0.940 101221. 5634.0 0.0055 >>> > 0.238 1.061 0.461 0.072 >>> > 3 0.0891 0.1016 0.941 101080. 5628.8 0.0052 >>> > 0.226 1.045 0.451 0.072 >>> > 4 0.0884 0.1011 0.942 100947. 5622.7 0.0050 >>> > 0.217 1.033 0.445 0.071 >>> > 5 0.0877 0.1006 0.942 100824. 5617.0 0.0049 >>> > 0.211 1.024 0.440 0.071 >>> > 6 0.0872 0.1001 0.943 100708. 5611.4 0.0047 >>> > 0.205 1.016 0.436 0.070 >>> > 7 0.0866 0.0997 0.943 100593. 5606.5 0.0047 >>> > 0.202 1.008 0.432 0.070 >>> > 8 0.0861 0.0992 0.944 100483. 5601.5 0.0046 >>> > 0.199 1.002 0.429 0.069 >>> > 9 0.0857 0.0989 0.944 100391. 5597.5 0.0045 >>> > 0.196 0.996 0.426 0.069 >>> > 10 0.0852 0.0985 0.944 100313. 5593.5 0.0045 >>> > 0.193 0.990 0.423 0.068 >>> > >>> > _________________________________________________________________ >>> > Explore the seven wonders of the world >>> > http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en- >>> > US&form=QBRE >>> > >>> >> >> >> >> -- >> MRC National Institute for Medical Research >> Division of Molecular Structure >> The Ridgeway, NW7 1AA, UK >> Email: [EMAIL PROTECTED] >> Phone: + 44 208 816 2515 >> > > -- > > *************************************************************** > * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com > * > * Global Phasing Ltd. > * Sheraton House, Castle Park > * Cambridge CB3 0AX, UK > *-------------------------------------------------------------- > * BUSTER Development Group (http://www.globalphasing.com) > *************************************************************** _________________________________________________________________ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE
