Many thanks for all the replies - I haven't yet tried all of them, but they all look worth following up on, much food for thought here:
* Several people suggested SITUS COLORES, which I shall certainly try and had not heard of until now. * The program ESSENS, from the Uppsala software factory, can perform a phased molecular replacement search which may be suitable for this kind of problem. * There were a couple of votes for the use of FFEAR, which I have tried unsuccessfully, although it is likely that I am not employing it correctly, it seems like a very versatile program. * The use of UCSF Chimera was suggested - I use chimera all the time for making figures, but had not thought of using it for docking, thanks for the suggestion. *Randy Read suggested a procedure involving cutting out the density that forms the search space, converting it to structure factors, then performing a rotation search in PHASER and a phased translation search using FFT to dock the model into the density. Cheers, Oliver.
