PHISTATS (CCP4: Supported Program)
NAMEphistats - Analysis of agreement between phase sets, and checking it against weighting factors.
SYNOPSISphistats HKLIN foo_in.mtz
[Keyworded input] OVERLAPMAP. INPUT AND OUTPUT FILES.
<nbin> is the number of resolution bins (equal width in [sin(theta)/(lambda)]**2) in which to divide partial structure data for normalization and sigmaA estimation. It is IMPORTANT that resolution ranges contain sufficient reflections. It is best to use as large a value of <nbin> as possible, as long as the estimates of sigmaA vary smoothly with resolution. If they do not, <nbin> should be reduced until sigmaA does vary smoothly. A good first guess is the number of reflections divided by 1000. If sigmaA refinement converges to zero in one or more of the ranges (which happens sometimes when the correct value is low), this can usually be circumvented by decreasing <nbin>.
Information about every <nmon>-th reflection will be written to the log file.
Defaults: 20 1000; maximum <nbin> allowed: 50.
PHI2 phases adjusted for a fractional Shift - especially useful when the two phase sets refer to different crystal origin:
PHI2_used = PHI2_input + 2PI(h X_fracshift + k Y_fracshift + l Z_fracshift)
PHI2 phases adjusted to change hand.
PHI2_used = -PHI2_shifted + 2PI(h CX + k CY + l CZ) where CX,CY,CZ are the centre of symmetry for this space group. (CX,CY,CZ) is (0,0,0) except for spacegroups I41, I4122, F4132,I4132. See reindexing notes.
INPUTThis is an MTZ file assigned to logical name HKLIN. The following column assignments are required:
PHIB2 may optionally be assigned. This is the second phase (degrees). If it is not assigned the program gives the correlation between WP and W2.
OUTPUTThere is no output file from this program.
Normally the program compares two sets of phases. They can be any set of phases you like, not just experimental phases against calculated model phases. Obviously, if you have calculated phases from a model there is no experimental weight. These phases are broken up into those from centric reflections and acentric.
Since centric reflections have a limited number of possible values PHISTATS compares the agreement between phases. That is if the phases are the same they agree but if they are different they disagree. Thus if the fraction that agree is unity then all the centric phases are equivalent.
The correlation with the weigths is exactly that. The linear correlation coefficient is calculated between the phase difference and a weight. It is calculated twice, once for WP and then W2. This coefficient can range between 1.0 and -1.0. The optimum set of weights would produce a correlation of -1.0 because this would mean that the largest weights would correspond to the smallest phase error. The linear correlation coefficient is also calculated between weight and cos(phase_difference).
There are similar calculations made for acentric reflections, however in this case a phase error or difference is calculated. Also, an estimated phase error is calculated. This is based on the principles used in SIGMAA where a quantity sigma_a is calculated. This is calculated from the two sets of structure factor magnitudes and need not be relevant.
Tables are produced where these quantities are compared against resolution and the value of the weight.
SEE ALSOoverlapmap, sigmaa
AUTHORSEleanor Dodson, University of York
# Assign weight 1 to FOM, weight 2 to FC magnitude. phistats hklin $CCP4_SCR/toxd_sf_mir << END TITLE Phase analysis RESOLUTION 40. 2. RANGES 10 500 LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 PHIBP=PHI_mir WP=W_mir - PHIB2=PHICtoxd W2=FCtoxd END
Phase analysis for alternative origin for mir phases and calculated ones
# Assign weight 1 to FOM, weight 2 to FC magnitude. phistats hklin $CCP4_SCR/toxd_sf_mir << END TITLE Phase analysis SHIFT 0.5 0.5 0.0 RESOLUTION 40. 2. RANGES 10 500 LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 PHIBP=PHI_mir WP=W_mir - PHIB2=PHICtoxd W2=FCtoxd END
Phase analysis for other hand
# Assign weight 1 to FOM, weight 2 to FC magnitude. phistats hklin $CCP4_SCR/toxd_sf_mir << END TITLE Phase analysis HAND RESOLUTION 40. 2. RANGES 10 500 LABIN FP=FTOXD3 SIGFP=SIGFTOXD3 PHIBP=PHI_mir WP=W_mir - PHIB2=PHICtoxd W2=FCtoxd END
phistats hklin os_lu_shhg2_pt_pt4_khg_os2_nat.mtz << END TITLE Phase analysis chmi model vs MIR phases RANGES 20 1000 ! Number of analysis bins, monitor interval RESOLUTION 100.0 2.6 ! Resolution limits in Angstroms LABIN FP=FP SIGFP=SIGFP WP=FOM PHIB2=PHI W2=FP END