F. Pavelcik

Department of Inorganic chemistry, Comenius University in Bratislava, Faculty of Natural Sciemces, 842 15 Bratislava, Slovak Republic



Electron density is easily interpreted if well-phased structure factor data are available to atomic resolution. If the data are below this resolution or the phasing is poor then "bones" skeletonization and chicken wire representation of the electron density are calculated. It is necessary to use computer graphics to interpret the electron density Map interpretation is a time limiting step in the protein structure determination an is quite subjective for low-resolution maps. Its automation is an important step in the overall automation of the protein structure determination and is essential for success of structure genomic projects.

A concept of flexible fragments has been developed for automatic building of crystal structures [1]. Six monopeptides (AlphaP0, Beta1P0, Beta2P0, GammaP0, BridgeP0, CisPro0) were designed as search fragments in a phased rotation and translation function for main chain building. Electron density in a crystal and in molecular fragments is expanded in spherical harmonics and normalized Bessel functions [2, 3]. A fast rotation function, which is calculated at each grid point of the asymmetric unit, is used to find the fragment orientation. Position, orientation and internal torsion angles are refined by a phased flexible refinement. Individual fragments are connected into chains. An algorithm for chain building is simplified using generalized atoms and virtual bonds. The structure is build from flexible groups rather than from individual atoms. A sequence is aligned by a combined marker and rotamer method. The side chains are built either by a combined marker & full conformation search or by the rotamer method. Side chains are independent structure units. The protein model is built with an accuracy of about 0.2Å at resolutions 1.2-2.1Å. A library of bioinorganic HET groups is currently under development. It is designed to build structures like ferredoxin and hemoglobin [4].


[1] F. Pavelcik. Acta Cryst., A59 (2003) 487-494.

[2] J. Friedman. Comput. Chem., 23 (1999) 9-23.

[3] F. Pavelcik, J. Zelinka, and Z. Otwinowski. Acta Cryst. D58, (2002) 275-283.

[4] F. Pavelcik, J. Molnar. Work in progress.