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Qs v.1.3: a parallel version of Queen of Spades
Author(s) -
Glykos Nicholas M.
Publication year - 2005
Publication title -
journal of applied crystallography
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.429
H-Index - 162
ISSN - 1600-5767
DOI - 10.1107/s0021889805011052
Subject(s) - queen (butterfly) , combinatorics , mathematics , zoology , biology , hymenoptera
The program Queen of Spades (Glykos & Kokkinidis, 2000; Glykos & Kokkinidis, 2001) encodes an algorithm for a stochastic multidimensional approach to molecular replacement. The program has been shown to be capable of successfully locating solutions even in cases as complex as a 23-dimensional 4-body problem (Glykos & Kokkinidis, 2003). Recently, we extended our approach to tackle the full molecular-replacement problem by allowing the possibility of using many different search models simultaneously, and showed that we could successfully locate solutions in the case of a 17-dimensional problem involving one DNA and two (different) protein search models (Glykos & Kokkinidis, 2004). This multimodel multidimensional approach does have its cost: with a few thousand unique reflections in a high-symmetry space group and with more than two search models, a typical Qs run would take well over two to three weeks of CPU time on the fastest personal workstations. The way forward for such computationally intensive calculations is of course parallelization. Here, I report the availability of a parallel version of Qs which is based on the Message Passing Interface (MPI) paradigm.