CrystalMaker Guide: Cambridge FDAT Files

The "FDAT" file format is used by the Cambridge Crystallographic Data Centre, for their widely-used Cambridge Structural Database (CSD) of organic structures. FDAT files are also generated by the Daresbury Crystallographic Database Service.

Example FDAT file

An example FDAT file is listed below:-

#AABHTZ 13770506 18 9 0 0 0 1 5 35 0 0 37132100000000000000000076 11372 10272 7359 10875 7107 9616333222 9 5 9 6 4 8 0 0 2P-1 240 R=0.0410 211 0121 0112 0 C 68H 23O 68N 68CL 99 CL1 -33550 9980 10610 CL2 -64070 -30840 32700 C1 -47750 3880 23070 C2 -57270 13370 34240 C3 -68450 9160 44830 C4 -70210 -4450 44470 C5 -60690 -13870 32950 C6 -49040 -10070 21810 C7 -38440 -19380 8860 N8 -36680 -29770 13510 N9 -26290 -38000 990 C10 -18570 -36530 -17520 N11 -21960 -38590 -33470 N12 -11480 -36040 -48430 C13 -2540 -32560 -40600 N14 -6420 -32680 -21040 N15 230 -28370 -7410 C16 -3050 -16060 7440 C17 4050 -12440 22150 O18 -11020 -8830 7930 C19 -23940 -48600 7180 C20 -33070 -50930 25480 O21 -14540 -55420 -2960 H2 -55800 23200 34700 H3 -75200 15700 53100 H4 -78400 -7800 53000 H7 -32600 -17500 -3200 H13 5700 -29600 -46900 H15 4600 -34000 -5700 H171 8100 -3600 21700 H172 10500 -19800 18900 H173 -600 -10700 33300 H201 -31300 -59800 27500 H202 -32900 -45100 37400 H203 -41300 -52500 24300 3 7 4 5 6 7 8 3 8 910111213141216171818112121 4 5 6 915171919192222221516

File Import

CrystalMaker extracts virtually all information contained in an FDAT file. Many of the header flags (e.g., errors, refinement, data collection) are interpreted, and diagnostic messages printed in the Notebook Window. Errors in unit cell parameters are also extracted, and used for bond-distance error propagation.

Symmetry

Although the spacegroup symbol and number is given, CrystalMaker prefers to use the symmetry operators instead-this avoids problems with non-standard settings! (A technical note: CrystalMaker does a lot of behind-the-scenes work converting the CSD symmetry operators to conventional G.E.P.'s: if there's a centre of symmetry at the origin we add the extra operators, and we also use the lattice type to "prune" the (redundant) symmetry operators corresponding to lattice translations. Thus, if one examines the imported G.E.P's using the Symmetry Options dialog, they should correspond to equivalent positions listed in the International Tables for Crystallography).

Atoms

CrystalMaker only imports atoms in the asymmetric unit; symmetry-generated atoms, if listed in the file, are ignored. The atom colours correspond to CrystalMaker's default atom colours: these can be edited or imported from a text file using the Elements dialog (Edit > Elements). If you import a large number of organic structures, we recommend importing the CSD Default Radii element table, and then saving these data in your preferences file.

Automatic Bond Generation

CrystalMaker uses a very concise way of representing bonding information-the bond specification cards. The individual bonds listed at the end of the FDAT file are therefore largely irrelevant. However, we search the bonds list to deduce the intended bonding pattern, and use this as a basis for CrystalMaker's own bond search. Thus, if the FDAT bond list contains C­C, C­H and C­O bonds, we create three separate bond specifications for these bonds. To determine the maximum bond lengths for each bond specification, we use the bond length tolerance in the CSD file (usually 0.40 Å) plus the sum of the atomic radii involved. Usually these radii are listed in the FDAT file. If the radii can't be found in the FDAT file, CrystalMaker searches its own default radii-these are the radii that appear in the Elements dialog. If a radius value still can't be found, a default value of 1.0 Åis used.

Because of the way CrystalMaker defines bonds, you may find that not all "requested" bonds can be found, and an alertbox will be displayed after the crystal has been imported. For example, if a molecule contains H-C and H-O bonds so that some H's are bonded to carbon but not oxygen, and vice versa, error messages will be printed in the output window. (Obviously, the carbon H will not have any bonds to O, and the oxygen H won't have any bonds to carbon). In these cases, you can disregard the messages.

If you still don't get the bonds you want, you can easily change the bonding specifications using the Edit Bond Specifications dialog.

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