Content:
The tool diff_fourier will be described that calculates different types of difference Fourier maps. We will not be dealing here with the normal difference ("Fo-Fc") or "2Fo-Fc" map that is used in model refinement and building, but rather with maps that use differences between measured amplitudes.
As long as BUSTER is installed, running
% diff_fourier -h
should bring up a help message.
Upon successful running, the script will create several output files - the prefix of which can be set with the -o flag.
Other potentially useful flags (for full details see output of -h):
Running
% diff_fourier -m truncate.mtz -p refine.mtz -P PH2FOFCWT FOM -o AnoFourier
will
If a PDB file (consistent with the phases) is also given with
% diff_fourier -m truncate.mtz -p refine.mtz -P PH2FOFCWT FOM -o AnoFourier -pdb refine.pdb
then
An example output looks like this:
============================================================================ mtz ......................................... truncate.mtz F ........................................... F SIGF ........................................ SIGF DANO ........................................ DANO SANO ........................................ SIGDANO pmtz ........................................ refine.mtz PHI ......................................... PH2FOFCWT FOM ......................................... FOM pdb ......................................... refine.pdb ... 7 peaks above 20 sigma 9 peaks above 15 sigma 11 peaks above 10 sigma 11 peaks above 8 sigma 12 peaks above 6 sigma 12 peaks above 5 sigma 37 peaks above 4 sigma -rw-r--r-- 1 vonrhein vonrhein 2132 Oct 10 15:29 AnoFourier.ANO.compare -rw-r--r-- 1 vonrhein vonrhein 13940 Oct 10 15:29 AnoFourier.ANO.hatom -rw-r--r-- 1 vonrhein vonrhein 24715 Oct 10 15:29 AnoFourier.ANO.pdb
AnoFourier.ANO.compare:
Peak Closest atom in refine.pdb [rms] Distance (<= 1.0 ) ------------------------------------------------------------------------- 31.23 <=> SE MSE F 7 ( 0.84 40.87) : 0.07 30.91 <=> SE MSE A 7 ( 0.84 45.76) : 0.04 30.22 <=> SE MSE A 126 ( 0.66 45.08) : 0.08 29.08 <=> SE MSE F 126 ( 0.66 40.55) : 0.13 23.72 <=> SE MSE F 137 ( 0.73 42.17) : 0.06 22.10 <=> SE MSE A 137 ( 0.73 45.81) : 0.13 21.10 <=> SE MSE F 293 ( 0.88 70.46) : 0.27 18.64 <=> SE MSE F 139 ( 0.58 47.16) : 0.32 16.20 <=> SE MSE A 293 ( 0.88 93.55) : 0.43 14.81 <=> SE MSE A 139 ( 0.58 53.66) : 0.26 11.24 <=> SE MSE F 1 ( 0.56 72.94) : 0.19 7.26 <=> SE MSE A 1 ( 0.56 92.71) : 0.49 4.10 <=> O THR A 161 ( 1.00 43.14) : 0.92 3.81 <=> CB THR F 261 ( 1.00 65.06) : 0.58 ...
AnoFourier.ANO.hatom:
ATOM Se -0.0623 -0.0435 0.3244 31.23 ATOM Se 0.0630 -0.0264 -0.2195 30.91 ATOM Se -0.0761 0.0141 -0.0840 30.22 ATOM Se 0.0776 0.0031 0.1880 29.08 ATOM Se -0.0028 -0.1375 0.2705 23.72 ATOM Se 0.0042 -0.1241 -0.1671 22.10 ATOM Se -0.0712 0.2201 0.1354 21.10 ATOM Se -0.0261 -0.1020 0.3066 18.64 ATOM Se 0.0787 0.2230 -0.0277 16.20 ATOM Se 0.0204 -0.0827 -0.2023 14.81 ATOM Se -0.3329 -0.1845 0.3639 11.24 ATOM Se 0.3373 -0.1699 -0.2602 7.26 ATOM Se 0.0752 -0.1320 0.2399 4.56 ...
AnoFourier.ANO.pdb:
CRYST1 62.827 90.075 191.529 90.00 90.00 90.00 P 21 21 21 SCALE1 0.015917 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011102 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005221 0.00000 ATOM 182 C DUM 1 -3.916 -3.917 62.136 1.00 31.23 11 ATOM 136 C DUM 2 3.955 -2.381 -42.043 1.00 30.91 11 ATOM 313 C DUM 3 -4.783 1.274 -16.088 1.00 30.22 11 ATOM 24 C DUM 4 4.875 0.282 36.013 1.00 29.08 11 ATOM 172 C DUM 5 -0.178 -12.385 51.807 1.00 23.72 11 ATOM 170 C DUM 6 0.264 -11.178 -32.014 1.00 22.10 11 ATOM 319 C DUM 7 -4.476 19.827 25.928 1.00 21.10 11 ATOM 173 C DUM 8 -1.639 -9.191 58.728 1.00 18.64 11 ATOM 33 C DUM 9 4.943 20.085 -5.303 1.00 16.20 11 ATOM 154 C DUM 10 1.282 -7.447 -38.744 1.00 14.81 11 ATOM 281 C DUM 11 -20.916 -16.621 69.699 1.00 11.24 11 ATOM 62 C DUM 12 21.190 -15.308 -49.836 1.00 7.26 11 ATOM 133 C DUM 13 4.726 -11.886 45.946 1.00 4.56 11 ...
So we have
If two sets of amplitudes are available, a difference Fourier map can be calculated with something like
% diff_fourier -m apo.mtz -p apo_refine.mtz -P PH2FOFCWT FOM -m2 inhibitor.mtz -o IsoFourier -pdb apo_refine.pdb -noANO -compare_cut 10.0
which
============================================================================ mtz ......................................... apo.mtz F ........................................... FP SIGF ........................................ SIGFP DANO ........................................ SANO ........................................ pmtz ........................................ apo_refine.mtz PHI ......................................... PH2FOFCWT FOM ......................................... FOM pdb ......................................... apo_refine.pdb mtz2......................................... inhibitor.mtz F2 .......................................... FP SIGF2 ....................................... SIGFP ... 0 peaks above 20 sigma 0 peaks above 15 sigma 0 peaks above 10 sigma 2 peaks above 8 sigma 3 peaks above 6 sigma 5 peaks above 5 sigma 20 peaks above 4 sigma -rw-r--r-- 1 vonrhein vonrhein 1846 Oct 10 15:56 IsoFourier.ISO.compare -rw-r--r-- 1 vonrhein vonrhein 6068 Oct 10 15:56 IsoFourier.ISO.hatom -rw-r--r-- 1 vonrhein vonrhein 10891 Oct 10 15:56 IsoFourier.ISO.pdb
This will show positive peaks where data in inhibitor.mtz predicts density that is absent in apo.mtz, eg. for an inhibitor:
IsoFourier.ISO.compare:
Peak Closest atom in apo.pdb [rms] Distance (<= 10.0 ) ------------------------------------------------------------------------- 9.37 <=> O HOH A 501 ( 1.00 27.89) : 1.97 8.72 <=> NZ LYS A 89 ( 1.00 43.51) : 0.87 6.85 <=> O HOH A 505 ( 1.00 44.68) : 2.09 5.99 <=> O HOH A 505 ( 1.00 44.68) : 1.68 5.48 <=> O HOH A 508 ( 1.00 41.07) : 2.34 4.85 <=> CB LYS A 89 ( 1.00 30.25) : 2.54 4.47 <=> CG2 ILE A 186 ( 1.00 12.12) : 1.45 ...
If we had already a model of the inhibitor and used that PDB file instead:
% diff_fourier -m apo.mtz -p apo_refine.mtz -P PH2FOFCWT FOM -m2 inhibitor.mtz -o IsoFourier -pdb inhibitor.pdb -noANO
we would get IsoFourier.ISO.compare:
Peak Closest atom in 2C6L/2c6l_shift.pdb [rms] Distance (<= 1.0 ) ------------------------------------------------------------------------- 9.37 <=> C10 DT4 A1299 ( 1.00 38.54) : 0.32 8.72 <=> S1 DT4 A1299 ( 1.00 54.82) : 0.31 6.85 <=> N5 DT4 A1299 ( 1.00 43.09) : 0.54 5.99 <=> C15 DT4 A1299 ( 1.00 47.69) : 0.81 5.48 <=> N7 DT4 A1299 ( 1.00 43.13) : 0.68 4.85 <=> CD LYS A 89 ( 1.00 43.87) : 0.56 4.32 <=> NZ LYS A 33 ( 1.00 41.01) : 0.68 4.26 <=> C PRO A 171 ( 1.00 30.06) : 0.84 4.02 <=> C4 DT4 A1299 ( 0.75 45.81) : 0.85 ...
showing us the peaks being very close to the inhibitor.