On Fri, Jun 4, 2010 at 2:28 AM, <[log in to unmask]> wrote: > I was using ccp4-6.0.2. I was using the following scripts: > sigmaa HKLIN test.mtz HKLOUT test-sigmaa.mtz << eof > title tt > labin FP=FP SIGFP=SIGFP FC=FP_atm PHIC=PHIC > labout DELFWT=DELFWT FWT=FWT WCMB=WCMB > symmetry P1211 > END > eof I get the same results, i.e. some FOMs (about 6%) have gone negative, and about 75% are exactly zero, whether I use the 6.0.2 version or the current one. This message in the output is pertinent: Correlation between E**2's is non-positive -- SIGMAA set to 0.05 Also this table (final iteration of optimization of sigma-A) is telling: Iteration Number 10 on SIGMAA OLD NEW MEAN D Limits SIGMAA Shift SIGMAA W 39.89 -- 8.74 0.00000 0.00000 0.00000 0.00000 8.74 -- 6.25 -0.59308 -0.00638 -0.59946 -0.45201 6.25 -- 5.13 0.66855 0.00000 0.66855 0.54835 5.13 -- 4.45 -0.61159 -0.00813 -0.61972 -0.49740 4.45 -- 3.99 0.71063 0.00000 0.71063 0.58634 3.99 -- 3.64 0.55934 0.00000 0.55934 0.43656 3.64 -- 3.37 0.00000 0.00000 0.00000 0.00000 3.37 -- 3.16 0.42551 0.00000 0.42551 0.32230 3.16 -- 2.98 0.00000 0.00000 0.00000 0.00000 2.98 -- 2.83 0.00000 0.00000 0.00000 0.00000 2.83 -- 2.69 0.00000 0.00000 0.00000 0.00000 2.69 -- 2.58 0.00000 0.00000 0.00000 0.00000 2.58 -- 2.48 0.00000 0.00000 0.00000 0.00000 2.48 -- 2.39 0.00000 0.00000 0.00000 0.00000 2.39 -- 2.31 0.00000 0.00000 0.00000 0.00000 2.31 -- 2.24 0.00000 0.00000 0.00000 0.00000 2.24 -- 2.17 0.00000 0.00000 0.00000 0.00000 2.17 -- 2.11 0.00000 0.00000 0.00000 0.00000 2.11 -- 2.05 0.00000 0.00000 0.00000 0.00000 2.05 -- 2.00 0.00000 0.00000 0.00000 0.00000 Refinement of SIGMAA has not converged -- using current values Overall MEAN W is 0.05260 DATA for SIGMAA PLOT STHOL**2 LN(SIGMAA) 0.008000 -0.402640 0.014211 -0.341601 0.017326 -0.580991 0.023544 -0.854478 ln(SigmaA) vs sthol**2 should give straight line with slope = -26.3189*(mean square coordinate error) and intercept = 0.5*ln(sigmap/sigman). > Is that possible that the negative FOM is due to the large discrepancy > between FP and FC? Thanks for your kindly help! Yes I think that's it: the Fo/Fc agreement is essentially random at high resolution, so the sigma-A plot data only goes up to ~ 6.5 Ang and is meaningless, i.e. this is a case of the method being inappropriate rather than a program bug. Perhaps others who have experience of using this program in this situation can comment, my experience is only cases where agreement is good. Cheers -- Ian