See also the tutorial worksheet.

3) Finding heavy atoms

Scaling and analysing datasets

This task can be used to scale datasets together, and assess the quality of the data and identify outliers. In this tutorial, we will use it to estimate f' and f'' for use in a later task.

Scale all against FP Comparison between wavelengths: F1 against F2/D2 gives Comparison for one wavelength: F1+ against F1- gives See Howell and Smith.

Preparing datasets for finding heavy atoms

Runs revise and ecalc, ready for rantan. Revise passes FM,SIGFM to Ecalc

Find heavy atoms

Spacegroup C2 Number of alternate origins: 4 This is a polar spacegroup: the origin is not fixed along the B axis Norigin Xo Yo Zo 1 0.0000 0.0000 0.0000 2 0.0000 0.0000 0.5000 3 0.5000 0.0000 0.0000 4 0.5000 0.0000 0.5000

Set 1: 

     0.26 0.06 0.75
     0.43 0.24 0.38
     0.20 0.45 0.36

Swap hand: 

     -0.26 -0.06 -0.75
     -0.43 -0.24 -0.38
     -0.20 -0.45 -0.36

Change origin to -0.5,-0.24,-0.5 

     0.24 0.18 0.75
     0.07 0.00 0.12
     0.30 0.79 0.14

Apply symop 1/2-X,1/2+Y,-Z to 3rd atom: 

     0.24 0.18 0.75
     0.07 0.00 0.12
     0.20 0.29 0.86
Which is set 2!!

Heavy atom refinement and phasing

EJD's jobs: infl always native, all 4 used as derivatives Data line--- resolution 15.0 2.8 deriv. centric. .ha sites refine 73. lrm y 72_1.ha (rantan,1st) 12 xyz,occ 74. lrm y 73_1.ha 10 (5,9 go) xyz,occ(odd cyc),b(even cyc) 75. lrm y 74_1.ha 11 (one new) xyz,occ(odd cyc),b(even cyc) 76. hrm y 75_1.ha 11 xyz,occ(odd cyc),b(even cyc) 77. 78. hrm y 74_1.ha 10 xyz,occ (bfac reset to 50) 79. lrm y 78_1.ha 10 xyz,occ 80. peak y 78_1.ha 10 xyz,occ 81. peak n 80_1.ha 10 aocc lrm 79_1.ha 10 aocc hrm 78_1.ha 10 aocc infl 78_infl.ha 10 aocc 82. peak n 81_1.ha 10 (other aocc lrm 81_2.ha 10 hand) aocc hrm 81_3.ha 10 aocc infl 81_4.ha 10 aocc

Or to summarise:

73
RANTAN solutions against lrm, centric
74
lose 2 sites, go again, and refine B
75
try 1 new site, but doesn't work
78
sites from 74, against hrm, centric
79
sites from 78, against lrm, centric
80
sites from 78, against peak, centric
81
all wavelengths, and refine aocc
82
as 81 but other hand