autostruct AMoRe
What is AMoRe? AMoRe at CCP4 Contact

What is AMoRe?

AMoRe is a software package for protein structure determination through molecular replacement.

The following text is from the October 2001 issue of Acta Crystallographica Section D: Biological Crystallography:

The most important features of AMoRe are the quality of the fast rotation and translation functions and the facility of multiple inputs to translation and rigid-body refinement functions, which allow for a fast multiple exploration of crystal configurations with a high level of automation.

The idea of molecular replacement is to build a tentative crystal structure using known molecular models similar to the actual molecules that constitute the crystal in order to start model building or refinement. The problem is to determine the positions of the models within the crystal cell. This is ultimately performed by comparing observed and calculated structure factors for selected positions of the independent molecules within the cell. In AMoRe, the comparison essentially involves the correlation coefficient in terms of amplitudes. This criterion was chosen in the light of the results available one decade ago, results that now may be considered as corresponding to easy or moderately difficult MR problems. At that time, an exhaustive positional search involving in general six variables per independent model using that simple but robust criterion could not be envisaged. Nowadays, a full six-dimensional search would also be too lengthy, although feasible. This explains, perhaps, the fact that the original ideas of Rossmann and Blow, i.e. the splitting of the search into two consecutive three-dimensional ones, are still found in filigree in most MR packages.

The main programs in AMoRe aim at selecting a certain number of positions, obtained through the exhaustive exploration of three-dimensional domains with fast functions, and computing the correlation coefficients associated with these positions. The idea is to assess many crystal configurations, as it is the contrast in the values of the criterion that gives one confidence in the solution. The fast functions, rotation functions and translation functions are either improved versions of already proposed ones or new ones. Accurate and fast algorithms are used throughout the package in order to save computing time. In particular, molecular scattering factors replace coordinates, which are used only once in the whole procedure.

The main stream in AMoRe is the set of values of the variables that specify the positions of the independent models within the crystal, from which structure factors and inputs to the fast functions are calculated. We will first define these variables and their relationship to the calculated structure factors. We will then describe the strategy for the selection of configurations.

AMoRe at CCP4

AMoRe is available through CCP4.

AMoRe originated with
Jorge Navaza
AMoRe adapted for CCP4 by
Eleanor Dodson
AMoRe into CCP4i by
Liz Potterton

The following text is part of the CCP4 program documentation for AMoRe:

AMORE (CCP4: Supported Program)

NAME

amore - Jorge Navaza's state-of-the-art molecular replacement package, updated February 1999.
The SORTFUN and TABFUN output are NOT compatible with the old version.
[Keyworded input]

DESCRIPTION

AMoRe includes routines to run a complete molecular replacement.

As well as carrying out ROTATION and TRANSLATION searches against various targets, and doing RIGID BODY REFINEMENT, there are routines to reformat the observed data from the new crystal form, and to generate and tabulate structure factors from the model in a large P1 cell. See reference [1].

The steps are usually carried out in the following order.

  1. The observed data is extended to cover a hemisphere of reciprocal space and reformatted.
  2. Structure factors for the model are tabulated on a fine grid (corresponding to a large "unit cell"). This is the key to the program's speed. All subsequent structure factors required for the searches are obtained by interpolating into this table. The structure factors can be calculated within Amore from a set of coordinates, using the option TABFUN, or generated outside the program and read in using the option SORTFUN.
  3. The rotation function is run searching for Patterson correlation within a sphere centred on the origin. This allows the Patterson to be expressed in terms of spherical harmonics, and the calculation to exploit FFT techniques. Two different types of indicators of a good solution are given:
    1. The correlation between the observed and model pattersons;
    2. Correlation coefficients and Rfactors between the observed Fs or Is and generated Fs or Is from a model with the given orientation.

REFERENCES

  1. J.Navaza, Acta Cryst. A50, 157-163 (1994)
    (General reference.)

Have a look at the entry for AMoRe in the Proceedings of the CCP4 Study Weekend 2001.

AMoRe from other sources

In case the CCP4 Suite of Programs is not directly available to you, or for other inquiries about AMoRe:

Mail Jorge Navaza