International
Tables for
Crystallography
Volume B
Reciprocal space
Edited by U. Shmueli

International Tables for Crystallography (2006). Vol. B, ch. 3.3, p. 383   | 1 | 2 |

Section 3.3.3.2.7. Frodo

R. Diamonda*

aMRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, England
Correspondence e-mail: rd10@cam.ac.uk

3.3.3.2.7. Frodo

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This system, due to Jones (Jones, 1978[link], 1982[link], 1985[link]; Jones & Liljas, 1984[link]), in its original implementation was a three-machine system comprising graphics display, minicomputer and mainframe, though more recent implementations combine the last two functions in a `midi'. Its capabilities are similar to those of Bilder described above, but its approach to stereochemical questions is very different. Where Bilder does not allow an atom to be moved out of context (unless it comprises a `chain' of one atom) Frodo will permit an atom or group belonging to a chain to be moved independently of the other members of the chain and then offers regularization procedures based on the method of Hermans & McQueen (1974[link]) to regain good stereochemistry. During this regularization, selected atoms may be fixed, remaining atoms then adjusting to these. A peptide, for example, may be inverted by moving the carbonyl oxygen across the peptide and fixing it, relying on the remaining atoms to rearrange themselves. (Bilder would do the equivalent operation by cutting the chain nearby, turning the peptide explicitly, reconnecting the chain and optimizing to regain chain continuity.) The Frodo approach is easy to use especially when large displacements of an existing structure are called for, but requires that ideal values be specified for all bond lengths, angles and fixed dihedrals since the system may need to regain such values in a distorted situation. Bilder, in contrast, never changes such features and so need not know their ideal values.

Frodo may work either with consecutive residues of a polymer chain, useful for initial building, or with a volume centred on a chosen position, which is ideal for adjusting interacting side chains which are close in space but remote in sequence.

In recent implementations Frodo can handle maps both in density grid form and in contour form and permits on-line contouring. It has also been developed (Jones & Liljas, 1984[link]) to allow the automatic adjustment of the position and orientation of small rigid groupings by direct reference to electron density in the manner of Diamond (1971[link]) but without the maintenance of chain continuity, which is subsequently reintroduced by regularization.

Horjales and Cambillau (Cambillau & Horjales, 1987[link]; Cambillau et al., 1984[link]) have also provided a development of Frodo which allows the optimization of the interaction of a ligand and a substrate with both molecules being treated as flexible.

References

Cambillau, C. & Horjales, E. (1987). TOM: a FRODO subpackage for protein-ligand fitting with interactive energy minimization. J. Mol. Graphics, 5, 174–177.Google Scholar
Cambillau, C., Horjales, E. & Jones, T. A. (1984). TOM, a display program for fitting ligands into protein receptors and performing interactive energy minimization. J. Mol. Graphics, 2, 53–54.Google Scholar
Diamond, R. (1971). A real-space refinement procedure for proteins. Acta Cryst. A27, 436–452.Google Scholar
Hermans, J. & McQueen, J. E. (1974). Computer manipulation of (macro) molecules with the method of local change. Acta Cryst. A30, 730–739.Google Scholar
Jones, T. A. (1978). A graphics model building and refinement system for macromolecules. J. Appl. Cryst. 11, 268–272.Google Scholar
Jones, T. A. (1982). FRODO: a graphics fitting program for macromolecules. In Computational crystallography, edited by D. Sayre, pp. 303–317. Oxford University Press.Google Scholar
Jones, T. A. (1985). Interactive computer graphics: FRODO. In Methods in enzymology, Vol. 115. Diffraction methods for biological molecules, Part B, edited by H. W. Wyckoff, C. H. W. Hirs & S. N. Timasheff, pp. 157–171. Orlando, Florida: Academic Press.Google Scholar
Jones, T. A. & Liljas, L. (1984). Crystallographic refinement of macromolecules having non-crystallographic symmetry. Acta Cryst. A40, 50–57.Google Scholar








































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