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Last Modified: Monday, 26-Nov-2012 11:32:25 EST

Qs -- Queen of Spades -- A stochastic approach to molecular replacement

Read the Caution

Consider using SoMORe instead.

Introduction (From Qs Documentation)

The program `Queen of Spades' (Qs from now on), is an attempt to write a multi-dimensional, multi-model, space-group general, molecular (re)placement program. The classical approach to the problem of placing n copies of m different search models in the asymmetric unit of a target structure, is to divide this 6n-dimensional problem into a succession of 3-dimensional searches (rotational search followed by translational search for the first model, followed by a rotational search and a translational search for the second model etc). Qs will attempt to solve this problem by a direct minimisation of a suitably chosen statistic (like the R-factor, or the correlation coefficient) in the 6n-dimensional space defined by the rotational and translational parameters of the n molecules. The minimisation algorithm is based on a modified reverse Monte Carlo procedure which is made (possibly) practical through (i) the calculation and in-core storage of the molecular transforms of the search models, and (ii) by keeping a table containing the contribution of each molecule to each reflection (thus making the CPU time per step independent of the number of molecules).

Running Qs in the Center for Structural Biology

No special setup is required. On any Core linux computer, invoke Qs with the command

    /srv/local/Qs/Qs/bin/Linux/intel-elf32-i386-static (inputfile)

To test Qs, you can:

    mkdir qtest
    cd qtest
    cp /srv/local/Qs/Qs/example/* .
The test should take several minutes, and converge on an R-factor of about 0.30.

Qs Documentation

Qs License and Reference

The following paragraphs are taken from the Glykos group website:

Queen of Spades is free software and you are encouraged to use, copy, modify, and distribute both the program and its documentation.

If you ever need to reference this program in your publications (but note that you are not required -at least by me- to do so), please use the following citation : Glykos, N.M. & Kokkinidis, M. (2000), ``A stochastic approach to Molecular Replacement'', Acta Crystallogr., D56, 169-174.

Last Modified: Monday, 26-Nov-2012 11:32:25 EST

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