NAME: Stefano Trapani
AFFILIATION: IBS Grenoble, France
CONTACT: stefano.trapani@ibs.fr
TITLE: "AMoRe: classical and modern"
ABSTRACT: An account is given of the latest developments of the AMoRe package. The newly introduced features follow the general guidelines that determined the success of the AMoRe molecular replacement (MR) strategy: a) the fast and accurate calculation of the main MR programs: rotation and translation functions, rigid-body refinement; b) the possibility of assessing a large number of trial crystal configurations, built up using automatic procedures.
Rotational searches by 3D FFT. The FFT calculation of spherical harmonics, Wigner D-matrices and rotation function has been extended to all angular variables. The resulting code avoids singularity issues arising from recursive formulas, performs faster and produces results with at least the same accuracy as the original code. It aims at permitting accurate and more rapid computations at high angular resolution for large particles like viruses.
Translational search in presence of NCS. An automatic selection/generation of NCS-related orientations has been introduced in the translation procedure.
Use of ensembles of structures as MR probes. In order to take advantage of the richness of structural information available nowadays, the additional program facility SUPER has been created for the automatic superposition of atomic structures - based on the correlation between their electron densities rather than their amino acid sequences - and the generation of ensembles of even remotely related molecular structures. Ensembles can be exploited (with no extra effort) as single MR probes, with the advantage that the regions of variability/flexibility of the molecules are implicitly weighted - with respect to the conserved regions - by the model itself. Indeed, ensembles of homologous molecules and/or different crystal forms of the same molecule can be more effective MR models than a single structure. Examples are presented.
Graphical interactive molecular replacement. A new graphical interface permits visual assessment of the crystal packing, with on-the-fly calculation of the correlation between calculated and experimental structure factor amplitudes. It aims at positioning small-size components of molecular complexes.