Hi, 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
