What
is AMoRe? |
AMoRe
at CCP4 |
Contact |
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*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* is available through CCP4.

AMoRe originated withJorge Navaza |
AMoRe adapted for CCP4 byEleanor Dodson |
AMoRe into CCP4i byLiz Potterton |

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

## AMORE (CCP4: Supported Program)## NAME
## DESCRIPTIONAMoRe 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. - The observed data is extended to cover a hemisphere of reciprocal space and reformatted.
- 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.
- 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:
- The correlation between the observed and model pattersons;
- Correlation coefficients and Rfactors between the observed Fs or Is and generated Fs or Is from a model with the given orientation.
## REFERENCES |

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

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

Mail Jorge Navaza |