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CCP4i: Graphical User Interface |
| MIR Tutorial Bath - MLPHARE / VECREF |
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Compute the isomorphous difference Pattersons for all derivatives to the maximum resolution of the derivative (i.e. without resolution cutoffs).
# fft HKLIN uffhscal MAPOUT ufdp <<EOD TITLE UF FH scaled native 3A isodif Patterson. PATT BIAS 1 ! Compensate for over-estimation of weak reflections. LABIN F1=FUF SIG1=SIGFUF F2=FNAT SIG2=SIGFNAT GRID 120 108 72 VF000 151447.56 ! "Volume" from FHSCAL output. EOD if ($status) exit fft HKLIN uafhscal MAPOUT uadp <<EOD TITLE UAc FH scaled native 3A isodif Patterson. PATT BIAS 1 LABIN F1=FUAC SIG1=SIGFUAC F2=FNAT SIG2=SIGFNAT GRID 120 108 72 VF000 151595.69 ! "Volume" from FHSCAL output. EOD if ($status) exit fft HKLIN usfhscal MAPOUT usdp <<EOD TITLE US FH scaled native 3A isodif Patterson. PATT BIAS 1 LABIN F1=FUS SIG1=SIGFUS F2=FNAT SIG2=SIGFNAT GRID 120 108 72 VF000 133105.75 ! "Volume" from FHSCAL output. EOD if ($status) exit fft HKLIN ptfhscal MAPOUT ptdp <<EOD TITLE PtCl FH scaled native 3A isodif Patterson. PATT BIAS 1 LABIN F1=FPTCL SIG1=SIGFPTCL F2=FNAT SIG2=SIGFNAT GRID 120 108 72 VF000 146681.38 ! "Volume" from FHSCAL output. EOD if ($status) exit fft HKLIN ybfhscal MAPOUT ybdp <<EOD TITLE YbCl FH scaled native 3A isodif Patterson. PATT BIAS 1 LABIN F1=FYBCL SIG1=SIGFYBCL F2=FNAT SIG2=SIGFNAT GRID 120 108 72 VF000 160414.22 ! "Volume" from FHSCAL output. EOD if ($status) exit fft HKLIN hgfhscal MAPOUT hgdp <<EOD TITLE PCMBS FH scaled native 3A isodif Patterson. PATT BIAS 1 LABIN F1=FPCMBS SIG1=SIGFPCMBS F2=FNAT SIG2=SIGFNAT GRID 120 108 72 VF000 150653.00 ! "Volume" from FHSCAL output. EOD
Again, note that the BIAS factor, whose function is to reduce the contribution to the Patterson of the weak high resolution reflections, which would otherwise contribute mainly noise, should only be used if the standard deviations of the amplitudes are reliable.
Provided there is no evidence of non-isomorphism, from the "best" Patterson, locate 1 or 2 major sites.
Refine with VECREF the site occupancies alone, then the occupancies and coordinates, then these plus the B parameters (this is all done in one job). Note that the site coordinates have been modified from those produced by the run of VECSUM (section 4.3.4.) with an origin shift of (0,½,0), together with a symmetry transformation of the space group. This was done purely to allow easy comparison of the resultant phases with those produced by the previous MLPHARE procedure.
# vecref MAPIN ufdp ATOUT ufvr.xyz <<EOD TITLE VECREF PBGD UF deriv - native. Isodif 3A. SPACEG P21212 RESOL 20 3 CYCLES 3 5 5 BREF ATOM U 1 1 .28 .18 .84 25 ATOM U 2 1 .68 .18 .34 25 EOD
Using MLPHARE in phase-only mode, calculate phases based on this derivative.
#
mlphare HKLIN pbgd_fhscal HKLOUT ufmp <<EOD
CYCLES 3
LABIN FP=FNAT SIGFP=SIGFNAT -
FPH1=FUF SIGFPH1=SIGFUF
LABOUT ALLIN
PRINT AVF AVE
DERIV UF
DCYCLE PHASE ALL
ATOM U 0.2864 0.1706 0.8346 1.0197 1.0197 BFAC 29.45
ATOM U 0.6840 0.1865 0.3449 0.6344 0.6344 BFAC 45.14
EOD
Using FFT and PEAKMAX, get all the peaks in the difference Fourier higher than a specified threshold (4s is suggested), with symmetry-related peaks eliminated. This can either be done by manually editing the logfile output from PEAKMAX, or writing a jiffy program to extract the sites, check for symmetry duplicates, and reformat the site coordinates ready for insertion into the VECREF script. The occupancies can be set all equal to 1, or better still, scaled in proportion to the peak heights; the B factors can be initialised to 25.
# fft HKLIN ufmp MAPOUT ufmpdf <<EOD TITLE UF diff Fourier phased on UF derivative refined by VECREF. LABIN F1=FUF SIG1=SIGFUF F2=FNAT SIG2=SIGFNAT PHI=PHIB W=FOM EOD if ($status) exit peakmax MAPIN ufmpdf <<EOD THRESH RMS 4 OUTPUT NONE EOD rm ufmpdf.map
Put all sites in together to refine with VECREF, as in step m.
The program will eliminate sites that either refine to low occupancy (e.g. < 2s), or to unrealistically low (e.g. < 0) or high (e.g. > 200) values of the B parameter.
# vecref MAPIN ufdp ATOUT ufvr1.xyz <<EOD TITLE VECREF PBGD UF deriv - native. Isodif 3A. SPACEG P21212 RESOL 20 3 CYCLES 3 5 10 BREF ATOM U 1 1 .28615 0.17076 0.83455 25 ATOM U 2 1 .68374 0.18610 0.34608 25 ATOM U 3 1 .18484 0.19094 0.89099 25 ATOM U 4 1 .28470 0.23418 0.83511 25 ATOM U 5 1 .28609 0.10676 0.83399 25 ATOM U 6 1 .28079 0.16491 0.94649 25 ATOM U 7 1 .50025 0.25000 0.61053 25 ATOM U 8 1 .28066 0.16519 0.72478 25 ATOM U 9 1 .78356 0.16182 0.40031 25 EOD
Repeat steps n and o, but calculate the cross-difference Fourier for the next derivative.
#
mlphare HKLIN pbgd_fhscal HKLOUT ufmp <<EOD
CYCLES 3
LABIN FP=FNAT SIGFP=SIGFNAT -
FPH1=FUF SIGFPH1=SIGFUF
LABOUT ALLIN
PRINT AVF AVE
DERIV UF
DCYCLE PHASE ALL
ATOM U 0.2859 0.1691 0.8332 1.4204 1.4204 BFAC 34.96
ATOM U 0.6825 0.1874 0.3440 0.5731 0.5731 BFAC 46.02
ATOM U 0.1846 0.1869 0.8877 0.4607 0.4607 BFAC 11.85
ATOM U 0.5005 0.2449 0.6131 0.4474 0.4474 BFAC 17.45
EOD
if ($status) exit
fft HKLIN ufmp MAPOUT uampdf <<EOD
TITLE UAc diff Fourier phased on UF derivative refined by VECREF.
LABIN F1=FUAC SIG1=SIGFUAC F2=FNAT SIG2=SIGFNAT PHI=PHIB W=FOM
EOD
if ($status) exit
peakmax MAPIN uampdf <<EOD
THRESH RMS 4
OUTPUT NONE
EOD
rm ufmp.mtz uampdf.map
Refine all sites together for this derivative, as in step p.
# vecref MAPIN uadp ATOUT uavr1.xyz <<EOD TITLE VECREF PBGD UAc deriv - native. Isodif 3A. SPACEG P21212 RESOL 20 3 CYCLES 3 5 10 BREF ATOM U 1 1 .28561 0.16973 0.83464 25 ATOM U 2 1 .18535 0.18616 0.88867 25 ATOM U 3 1 .49905 0.25000 0.61358 25 ATOM U 4 1 .68243 0.18754 0.34529 25 ATOM U 5 1 .28067 0.10440 0.83276 25 ATOM U 6 1 .04065 0.25000 0.46040 25 ATOM U 7 1 .28534 0.23489 0.82928 25 EOD
Add all the new refined sites for the new derivative to the input for MLPHARE.
Repeat steps q and r for each of the remaining derivatives.
#
mlphare HKLIN pbgd_fhscal HKLOUT uamp <<EOD
CYCLES 3
LABIN FP=FNAT SIGFP=SIGFNAT -
FPH1=FUF SIGFPH1=SIGFUF -
FPH2=FUAC SIGFPH2=SIGFUAC
LABOUT ALLIN
PRINT AVF AVE
DERIV UF
DCYCLE PHASE ALL
ATOM U 0.2859 0.1691 0.8332 1.4204 1.4204 BFAC 34.96
ATOM U 0.6825 0.1874 0.3440 0.5731 0.5731 BFAC 46.02
ATOM U 0.1846 0.1869 0.8877 0.4607 0.4607 BFAC 11.85
ATOM U 0.5005 0.2449 0.6131 0.4474 0.4474 BFAC 17.45
DERIV UAc
DCYCLE PHASE ALL
ATOM U 0.2881 0.1705 0.8453 0.7896 0.7896 BFAC 41.58
ATOM U 0.1844 0.1846 0.8904 0.9079 0.9079 BFAC 16.16
ATOM U 0.4855 0.2383 0.6310 0.5954 0.5954 BFAC 22.73
ATOM U 0.6819 0.1883 0.3428 0.2363 0.2363 BFAC 37.83
ATOM U 0.0398 0.2416 0.4586 0.7912 0.7912 BFAC 45.86
EOD
if ($status) exit
fft HKLIN uamp MAPOUT usmpdf <<EOD
TITLE US diff Fourier phased on UF & UAc derivatives refined by VECREF.
LABIN F1=FUS SIG1=SIGFUS F2=FNAT SIG2=SIGFNAT PHI=PHIB W=FOM
EOD
if ($status) exit
peakmax MAPIN usmpdf <<EOD
THRESH RMS 4
OUTPUT NONE
EOD
rm uamp.mtz usmpdf.map
#
vecref MAPIN usdp ATOUT usvr1.xyz <<EOD
TITLE VECREF PBGD US deriv - native. Isodif 3A.
SPACEG P21212
RESOL 20 3
CYCLES 3 5 10
BREF
ATOM U 1 1 .18184 0.19281 0.88767 25
ATOM U 1 1 .28535 0.17936 0.83471 25
ATOM U 1 1 .66149 0.13307 0.90081 25
ATOM U 1 1 .69055 0.17053 0.85079 25
ATOM U 1 1 .87630 0.05247 0.65764 25
ATOM U 1 1 .49026 0.23516 0.63313 25
ATOM U 1 1 .71442 0.13248 0.76857 25
ATOM U 1 1 .67905 0.03676 0.10827 25
ATOM U 1 1 .89558 0.14894 0.14228 25
ATOM U 1 1 .78685 0.17541 0.81784 25
EOD
#
mlphare HKLIN pbgd_fhscal HKLOUT usmp <<EOD
CYCLES 3
LABIN FP=FNAT SIGFP=SIGFNAT -
FPH1=FUF SIGFPH1=SIGFUF -
FPH2=FUAC SIGFPH2=SIGFUAC -
FPH3=FUS SIGFPH3=SIGFUS
LABOUT ALLIN
PRINT AVF AVE
DERIV UF
DCYCLE PHASE ALL
ATOM U 0.2859 0.1691 0.8332 1.4204 1.4204 BFAC 34.96
ATOM U 0.6825 0.1874 0.3440 0.5731 0.5731 BFAC 46.02
ATOM U 0.1846 0.1869 0.8877 0.4607 0.4607 BFAC 11.85
ATOM U 0.5005 0.2449 0.6131 0.4474 0.4474 BFAC 17.45
DERIV UAc
DCYCLE PHASE ALL
ATOM U 0.2881 0.1705 0.8453 0.7896 0.7896 BFAC 41.58
ATOM U 0.1844 0.1846 0.8904 0.9079 0.9079 BFAC 16.16
ATOM U 0.4855 0.2383 0.6310 0.5954 0.5954 BFAC 22.73
ATOM U 0.6819 0.1883 0.3428 0.2363 0.2363 BFAC 37.83
ATOM U 0.0398 0.2416 0.4586 0.7912 0.7912 BFAC 45.86
DERIV US
DCYCLE PHASE ALL
ATOM U 0.1826 0.1927 0.8884 0.7042 0.7042 BFAC 30.66
EOD
if ($status) exit
fft HKLIN usmp MAPOUT ptmpdf <<EOD
TITLE PtCl diff Fourier phased on UF, UAc & US derivatives refined by VECREF.
LABIN F1=FPTCL SIG1=SIGFPTCL F2=FNAT SIG2=SIGFNAT PHI=PHIB W=FOM
EOD
if ($status) exit
peakmax MAPIN ptmpdf <<EOD
THRESH RMS 4
OUTPUT NONE
EOD
rm usmp.mtz ptmpdf.map
#
vecref MAPIN ptdp ATOUT ptvr1.xyz <<EOD
TITLE VECREF PBGD PtCl deriv - native. Isodif 3A.
SPACEG P21212
RESOL 20 3
CYCLES 3 5 10
BREF
ATOM PT 1 1 .25247 0.04321 0.40324 25
ATOM PT 2 1 .17795 0.20318 0.89739 25
ATOM PT 3 1 .15464 0.04206 0.53930 25
ATOM PT 4 1 .28551 0.13117 0.84088 25
ATOM PT 5 1 .28334 0.20094 0.83942 25
ATOM PT 6 1 .18329 0.15558 0.91884 25
ATOM PT 7 1 .08052 0.23379 0.40924 25
ATOM PT 8 1 .12630 0.15489 0.41827 25
ATOM PT 9 1 .28262 0.16810 0.76787 25
ATOM PT 10 1 .00000 0.00000 0.53845 25
EOD
#
mlphare HKLIN pbgd_fhscal HKLOUT ptmp <<EOD
CYCLES 3
LABIN FP=FNAT SIGFP=SIGFNAT -
FPH1=FUF SIGFPH1=SIGFUF -
FPH2=FUAC SIGFPH2=SIGFUAC -
FPH3=FUS SIGFPH3=SIGFUS -
FPH4=FPTCL SIGFPH4=SIGFPTCL
LABOUT ALLIN
PRINT AVF AVE
DERIV UF
DCYCLE PHASE ALL
ATOM U 0.2859 0.1691 0.8332 1.4204 1.4204 BFAC 34.96
ATOM U 0.6825 0.1874 0.3440 0.5731 0.5731 BFAC 46.02
ATOM U 0.1846 0.1869 0.8877 0.4607 0.4607 BFAC 11.85
ATOM U 0.5005 0.2449 0.6131 0.4474 0.4474 BFAC 17.45
DERIV UAc
DCYCLE PHASE ALL
ATOM U 0.2881 0.1705 0.8453 0.7896 0.7896 BFAC 41.58
ATOM U 0.1844 0.1846 0.8904 0.9079 0.9079 BFAC 16.16
ATOM U 0.4855 0.2383 0.6310 0.5954 0.5954 BFAC 22.73
ATOM U 0.6819 0.1883 0.3428 0.2363 0.2363 BFAC 37.83
ATOM U 0.0398 0.2416 0.4586 0.7912 0.7912 BFAC 45.86
DERIV US
DCYCLE PHASE ALL
ATOM U 0.1826 0.1927 0.8884 0.7042 0.7042 BFAC 30.66
DERIV PtCl
DCYCLE PHASE ALL
ATOM PT 0.2507 0.0452 0.4118 1.2751 1.2751 BFAC 49.26
ATOM PT 0.1676 0.1937 0.9093 0.4910 0.4910 BFAC 96.21
ATOM PT 0.1568 0.0414 0.5378 0.7443 0.7443 BFAC 55.40
ATOM PT 0.1490 0.1411 0.9022 0.4471 0.4471 BFAC 74.56
ATOM PT 0.0770 0.2304 0.4085 0.3281 0.3281 BFAC 50.08
ATOM PT 0.1217 0.1374 0.4133 0.3520 0.3520 BFAC 19.55
EOD
if ($status) exit
fft HKLIN ptmp MAPOUT ybmpdf <<EOD
TITLE YbCl diff Fourier phased on UF, UAc, US & Pt derivatives.
LABIN F1=FYBCL SIG1=SIGFYBCL F2=FNAT SIG2=SIGFNAT PHI=PHIB W=FOM
EOD
if ($status) exit
peakmax MAPIN ybmpdf <<EOD
THRESH RMS 4
OUTPUT NONE
EOD
rm ptmp.mtz ybmpdf.map
#
vecref MAPIN ybdp ATOUT ybvr1.xyz <<EOD
TITLE VECREF PBGD YbCl deriv - native. Isodif 3A.
SPACEG P21212
RESOL 20 3
CYCLES 3 5 10
BREF
ATOM YB 1 1 .49373 0.23695 0.61978 25
ATOM YB 2 1 .18322 0.18647 0.88976 25
ATOM YB 3 1 .28605 0.16971 0.83379 25
ATOM YB 4 1 .98864 0.25000 0.38272 25
ATOM YB 5 1 .00927 0.05067 0.47647 25
ATOM YB 6 1 .87544 0.03871 0.63246 25
ATOM YB 7 1 .95501 0.13334 0.16714 25
ATOM YB 8 1 .24534 0.06416 0.15415 25
ATOM YB 9 1 .68375 0.18664 0.33213 25
EOD
Use MLPHARE in phased refinement mode with the anomalous data to detect the correct hand, as previously described.
If necessary, correct the input coordinates and set the anomalous occupancy of each atom to its real occupancy.
Using MLPHARE in phasing-only mode, calculate phases based on all derivatives (again, the PCMBS derivative was omitted).
#
mlphare HKLIN pbgd_fhscal HKLOUT allmp1 <<EOD
CYCLES 3
LABIN FP=FNAT SIGFP=SIGFNAT -
FPH1=FUF SIGFPH1=SIGFUF -
FPH2=FUAC SIGFPH2=SIGFUAC -
FPH3=FUS SIGFPH3=SIGFUS -
FPH4=FPTCL SIGFPH4=SIGFPTCL -
FPH5=FYBCL SIGFPH5=SIGFYBCL
LABOUT ALLIN
PRINT AVF AVE
DERIV UF
DCYCLE PHASE ALL
ATOM U 0.2859 0.1691 0.8332 1.4204 1.4204 BFAC 34.96
ATOM U 0.6825 0.1874 0.3440 0.5731 0.5731 BFAC 46.02
ATOM U 0.1846 0.1869 0.8877 0.4607 0.4607 BFAC 11.85
ATOM U 0.5005 0.2449 0.6131 0.4474 0.4474 BFAC 17.45
DERIV UAc
DCYCLE PHASE ALL
ATOM U 0.2881 0.1705 0.8453 0.7896 0.7896 BFAC 41.58
ATOM U 0.1844 0.1846 0.8904 0.9079 0.9079 BFAC 16.16
ATOM U 0.4855 0.2383 0.6310 0.5954 0.5954 BFAC 22.73
ATOM U 0.6819 0.1883 0.3428 0.2363 0.2363 BFAC 37.83
ATOM U 0.0398 0.2416 0.4586 0.7912 0.7912 BFAC 45.86
DERIV US
DCYCLE PHASE ALL
ATOM U 0.1826 0.1927 0.8884 0.7042 0.7042 BFAC 30.66
DERIV PtCl
DCYCLE PHASE ALL
ATOM PT 0.2507 0.0452 0.4118 1.2751 1.2751 BFAC 49.26
ATOM PT 0.1676 0.1937 0.9093 0.4910 0.4910 BFAC 96.21
ATOM PT 0.1568 0.0414 0.5378 0.7443 0.7443 BFAC 55.40
ATOM PT 0.1490 0.1411 0.9022 0.4471 0.4471 BFAC 74.56
ATOM PT 0.0770 0.2304 0.4085 0.3281 0.3281 BFAC 50.08
ATOM PT 0.1217 0.1374 0.4133 0.3520 0.3520 BFAC 19.55
DERIV YbCl
DCYCLE PHASE ALL
ATOM YB 0.4938 0.2410 0.6152 0.8800 0.8800 BFAC 33.38
EOD
Repeat all the difference Fouriers and the VECREF refinements as in steps o and p.
Repeat steps u and v until a consistent set of sites is attained (3 iterations).
#
mlphare HKLIN pbgd_fhscal HKLOUT allmp4 <<EOD
CYCLES 5
LABIN FP=FNAT SIGFP=SIGFNAT -
FPH1=FUF SIGFPH1=SIGFUF DPH1=DANUF SIGDPH1=SIGDANUF -
FPH2=FUAC SIGFPH2=SIGFUAC DPH2=DANUAC SIGDPH2=SIGDANUAC -
FPH3=FUS SIGFPH3=SIGFUS -
FPH4=FPTCL SIGFPH4=SIGFPTCL DPH4=DANPTCL SIGDPH4=SIGDANPTCL -
FPH5=FYBCL SIGFPH5=SIGFYBCL -
FPH6=FPCMBS SIGFPH6=SIGFPCMBS DPH6=DANPCMBS SIGDPH6=SIGDANPCMBS
LABOUT ALLIN
PRINT AVF AVE
DERIV UF
DCYCLE PHASE ALL
ATOM U 0.2857 0.1706 0.8364 1.0553 1.0553 BFAC 31.71
ATOM U 0.1843 0.1875 0.8893 0.5338 0.5338 BFAC 19.32
ATOM U 0.5004 0.2448 0.6133 0.4753 0.4753 BFAC 17.22
ATOM U 0.6822 0.1878 0.3420 0.6059 0.6059 BFAC 51.09
ATOM U 0.9892 0.0538 0.4883 0.2830 0.2830 BFAC 29.83
DERIV UAc
DCYCLE PHASE ALL
ATOM U 0.1848 0.1849 0.8905 0.9219 0.9219 BFAC 17.69
ATOM U 0.2888 0.1707 0.8472 0.6473 0.6473 BFAC 26.28
ATOM U 0.4857 0.2386 0.6317 0.6174 0.6174 BFAC 21.81
ATOM U 0.0400 0.2422 0.4582 0.8310 0.8310 BFAC 49.24
ATOM U 0.6796 0.1902 0.3431 0.2445 0.2445 BFAC 35.64
ATOM U 0.9832 0.0503 0.4903 0.4344 0.4344 BFAC 45.67
ATOM U 0.9691 0.0262 0.1006 0.3802 0.3802 BFAC 61.76
DERIV US
DCYCLE PHASE ALL
ATOM U 0.1826 0.1933 0.8889 0.7029 0.7029 BFAC 29.99
DERIV PtCl
DCYCLE PHASE ALL
ATOM PT 0.2507 0.0452 0.4117 1.2707 1.2707 BFAC 49.47
ATOM PT 0.1569 0.0412 0.5374 0.7500 0.7500 BFAC 55.47
ATOM PT 0.1216 0.1371 0.4125 0.3743 0.3743 BFAC 26.08
ATOM PT 0.1649 0.1971 0.9063 0.4686 0.4686 BFAC 81.33
ATOM PT 0.0769 0.2298 0.4087 0.3164 0.3164 BFAC 49.01
ATOM PT 0.1509 0.1408 0.9052 0.4554 0.4554 BFAC 72.34
DERIV YbCl
DCYCLE PHASE ALL
ATOM YB 0.4976 0.2364 0.6143 0.5937 0.5937 BFAC 36.75
ATOM YB 0.1983 0.1838 0.9253 0.1541 0.1541 BFAC 26.52
ATOM YB 0.0106 0.0529 0.4774 0.1843 0.1843 BFAC 21.92
DERIV PCMBS
DCYCLE PHASE ALL
ATOM HG 0.0723 0.0646 0.1533 0.3838 0.3838 BFAC 35.06
ATOM HG 0.2452 0.0609 0.1442 0.2874 0.2874 BFAC 31.25
ATOM HG 0.7974 0.1644 0.7249 0.2557 0.2557 BFAC 63.77
EOD
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