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 <[EMAIL PROTECTED]> 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) ***************************************************************
