Open AccessModel preparation in MOLREP and examples of model improvement using X‐ray data
Author(s) -
Lebedev Andrey A.,
Vagin Alexei A.,
Murshudov Garib N.
Publication year - 2008
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444907049839
Subject(s) - molecular replacement , context (archaeology) , model building , molecular model , computer science , function (biology) , algorithm , chemistry , crystallography , physics , crystal structure , stereochemistry , biology , paleontology , quantum mechanics , evolutionary biology
The success of molecular replacement is critically dependent on the quality of the search model. Several model‐preparation procedures are integrated in the molecular‐replacement program MOLREP . These include model modification on the basis of amino‐acid sequence alignment and model correction based on analysis of the solvent‐accessibility of the atoms. The packing function used in MOLREP for the translational search is explained in the context of model preparation. In difficult cases, bioinformatics‐based modifications are not sufficient for successful molecular replacement. An approach implemented in MOLREP for solving cases with translational noncrystallographic symmetry is an example of model preparation in which analysis of X‐ray data plays an essential role. In addition, two examples are presented in which the X‐ray data were used to refine partial models for subsequent use in molecular replacement.