Application of constrained real-space refinement of flexible molecular fragments to automatic model building of RNA structures

New methods have been developed for locating phosphate groups and nucleic acid bases in the electron density of RNA structures. These methods utilize a constrained real-space refinement of molecular fragments and a phased rotation-conformation-translation function. Real-space refinement has also contributed to the improvement of the bone/base method of RNA model building and to redesigning the method of building double helices in nucleic acid structures. This improvement is reflected in the increased accuracy of the model building and the ability to better distinguish between correct and false solutions. A program, RSR, was created, and the programs NUT, HEL and DHL were upgraded and organized into a program system, which is CCP4 oriented. Source codes will also be released.