The main structure aligner in the CCP4 Software Suite, SSM (Secondary Structure Matching) has a limited applicability on the intermediate stages of the structure solution process, when the secondary structure cannot be reliably computed due to structural incompleteness or a fragmented mainchain. In this study, we describe a new algorithm for the alignment and comparison of protein structures in CCP4, which was designed to overcome SSM's limitations but retain its quality and speed. The new algorithm, named GESAMT (General Efficient Structural Alignment of Macromolecular Targets), employs the old idea of deriving the global structure similarity from a promising set of locally similar short fragments, but uses a few technical solutions that make it considerably faster. A comparative sensitivity and selectivity analysis revealed an unexpected significant improvement in the fold recognition properties of the new algorithm, which also makes it useful for applications in the structural bioinformatics domain. The new tool is included in the CCP4 Software Suite starting from version 6.3.