Using FOX for Ab Initio Structure Determination: step-by-step tutorial

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C   1
N   1 1.465
C   2 1.366  1 119.987
N   3 1.321  2 120.030  1   6.0
C   4 1.355  3 119.982  2   6.8
N   5 1.136  4 180.000  3  46.3
N   3 1.366  2 120.022  1 186.0
C   7 1.466  3 119.988  2 354.9
C   8 1.529  7 109.482  3 185.0
S   9 1.814  8 109.456  7 180.0
C  10 1.815  9  99.984  8 180.0
C  11 1.507 10 109.466  9 180.0
N  12 1.341 11 126.014 10  90.0
C  13 1.305 12 109.239 11 180.0
N  14 1.349 13 108.723 12 360.0
C  12 1.347 11 125.981 10 269.7
C  16 1.507 12 126.567 11   0.2
This file can be created from other formats (eg .pdb) using babel . For example, to convert from pdb to fhz, use: "babel -ipdb cime.pdb -ofhz cime.fhz -d"
Note that after importing, there are tight limits set other all bond lengths/angles/dihedral angles. You should remove the limits manually for the free torsion bonds (right-click on each parameter to change these limits or remove them).
Note: I still recomend to input manually any molecule rather than using a zmatrix automatically created from a pdb or another source file. That way, you can choose the order of the atoms, and Iadvise you to put (as possible) the more flexible parts of the molecule at the end(s) of the Z-matrix . This way your optimization should run better.


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