Hi Partha, It sounds to me as though the amplitudes that were given to resolve as FP may have been calculated ones. The FP and SIGFP written out by resolve are normally the same as those that are input, and so you can use them in refinement in most circumstances. You are always safest to do as Garib suggests and to use your original FOBS SIGFOBS data in refinement.
All the best, Tom T > > Just a newbie question: > > Could someone explain what might have gone wrong in this case? I guess > the structure factors should not change anyway! I am a bit confused > because I have used solve resolve several times for experimental > phasing, never had such a problem, on the other hand, have not heard > about density modification for MR apart from one posting (from Prof. > Lawrence Perl I think). > > 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.. > > 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 >
