Rossmann's Lab

Molecular Replacement Programs

Molecular replacement is one of the most useful technitques for the solution of macromolecular structures, using non-crystallographic symmetry. The principles of non-crystallographic symmetry were proposed by Rossmann and Blow (1962) [1].

[1] Rossman,M.G & Blow,D.M. 1962. The Detection of Sub-Units within the Crystallographic Asymmetric Unit. Acta Cryst. 15:24-32.

GLRF

GLRF is a General locked rotation function program [2,3]. This program calculates the general locked rotation function. The self-rotation function determines non-crystallographic symmetry in a crystall. The cross-rotation function determines the orientation relationship of a structure in one unit cell to similar structures in another cell. Since the relationship between the assumed molecular symmetry axes is 'locked', the program can greatly enhance the signal peaks on the rotation function. Therefore, it is much more powerful for assemblies with high local symmetry, such as icosahedral viruses. This program was developed by Liang Tong.

Download the GLRF from the Author's page, or contact the Author for downloading.

[2] Rossmann,M.G., Ford,G.C., Watson,H.C., & Banaszak,L.J. 1972. Molecular Symmetry of Glyceraldehyde-3-phosphate Dehydrogenase - Appendix. The Locked Rotation Function. J. Mol. Biol. 64:237-249.

[3] Tong,T. & Rossmann,M.G. 1972. The Locked Rotation Function. Acta Cryst. A46:783-792.

TRANSF

TRANSF is a Translation function program [4]. This program searches for the best position of a molecule, rotated from one cell (refered to as h cell), in the reference (1st) asymmetric unit of another cell (refered to as p cell). It rotates the electron density (e.g. a 3D electron microscopy image) into the first (refernce) assymetric unit of p cell. This molecule is then multiplied by the crystallographic symmetry of p cell. R factors can then be calculated for the molecule situated at a stated position in the reference asymmetric unit. A search can be made to find the lowest R factor or a set of translation function Fourier coefficients can be set up. The corresponding function should then have a maximum at the best position of the molecule. In general, a translation Function will show a reasonable molecular position which can the be explored by means of a fine R factor search.

Download TRANSF source and man page (keyworded)

Download TRANSF test files (keyworded)

Download TRANSF source and man page (non-keyworded)

Download TRANSF test files (non-keyworded)

[4] Argos,P. & Rossmann,M.G. 1980. in Thery and Practice of Direct Methods in Crystallography (edited by Laddand Palmer)

TF

TF is a new version of the translation function program by Liang Tong.

Download the GLRF from the Author's page, or contact the Author for downloading.

ENVELOPE

ENVELOPE is a Real Space Molecular averaging and Envelope Finding program [5]. This program is used for the following purposes:

Given the crystallographic symmetry and molecular radius find the way the spheres touch. Use the shortest distance to any center to determine which grid point belongs to what molecule (or solvent if outside any envelope).
Makes a mask corresponding to an input density in cell h.
Given the mask modify the map in cell p by :

adjust density in solvent.
adjust density in nucleic acid.
average protein density, given the non-cryst. symmetry.

Put modified density in p cell back into h cell in a standard orientation. This can then be used both for defining an improved envelope and for viewing.

Download ENVELOPE source and man page (keyworded)

Download ENVELOPE test files (keyworded)

Download ENVELOPE source and man page (non-keyworded)

[4] Rossmann,M.G., McKenna,R., Tong,L., Xia,D., Dai,J.B., Wu,H. and Choi,H. 1992. Molecular Replacement Real-Space Averaging. J. Appl. Cryst. 25:166-180.

RECIP

RECIP is a Reciprocal sapce data statistics program. This program gives statistics and makes combination of observations and calculated structure factors from the Fftinv program. The new phases, usually from the last cycle of molecular replacement are incorporated into the diffraction dataset with weights for the construction of the next density model. The weights are calculated as 'figure-od-merits' in accordance with 'errors'- the difference between observed and calculated structure amplitudes. The output data is written to a new FIT file. This program is one of the basic steps in molecular replacemen cycling.