Arnon, We have developed an MR search mechanism which may be helpful in this scenario. It is web accessible and available to any public or academic researchers:
https://portal.nebiogrid.org/secure/apps/wsmr/ It can use up to the full set of SCOP domains (100k) to attempt a Phaser MR placement of each domain and then ranks the results, allowing you to identify a single well placed domain. The web-based system does not allow you to fix that domain to continue the search for subsequent domains but we can do this from the command line interface. If you have a particular set of domains you'd like to search against (RCSB or SCOP PDB codes), then we can limit the search to that set. If you decide to use this, please contact us once your first domain search has been completed (these take 2-3 years of serial computing time and will finish in 1-3 days, depending on how many other computations are ahead of it in our queue, the complexity/resolution of your data set, space group, and unit cell size). Regards, Ian Stokes-Rees
