SOMoRe -- Search and Optimization for Molecular Replacement

Brief Description

SOMoRe is a molecular replacement program, based on Qs (Queen of Spades). The simulated annealing approach of QS is replaced by a different, deterministic approach. Both approaches use a course, 6D global search and multi-start optimization. But, read the documentation.

Running SOMoRe

The SOMoRe programs (pack, somore, writepdb) are located in /srv/local/linux/bin, which should be in your path on Core linux computers. You should run SOMoRe by creating a command file and submitting it to a batch queue on one of the crunch computers.

Documentation

See somore.pdf.

From the Author

We are eager to distribute SOMoRe so that others can also test its ability to solve difficult MR problems and help us refine the code. If you are able to solve a difficult problem that has resisted other methods, we'd love to hear back from you!

In return, when reporting on a new structure that was solved with the help of SOMoRe, we would ask that you would mention SOMoRe and cite the Acta. Cryst. article that introduces SOMoRe:

Jamrog, D. C., Phillips, G. N. Jr., Zhang, Y. (2003), SOMoRe: a multi-dimensional search and optimization approach to molecular replacement, Acta Cryst. D59, 304---314.

I should note that if the unit cell is very large that the run time of SOMoRe might be too long. Please check out the manual available from the Somore webpage on how to estimate the run time to see if it will be reasonable. We are currently working on a parallelized version of the code so check back to the web site periodically.

Finally, SOMoRe is in a state of development, so if you find any bugs, please email us. Also, you may want to periodically check the web page, www.caam.rice.edu/~djamrog/somore.html, for the most current version available by email request from somore@xtal.biochem.wisc.edu.

Diane Jamrog (Comp. & Applied Math Dept., Rice University, Houston, TX)
Gary Wessenberg (Biochemistry Dept., University of Wisconsin, Madison, WI)

Last Modified: Monday, 25-Jul-2005 14:43:19 EDT

RC Home | Search | Table of Contents | General Information

Richards Center (www.rc.yale.edu) at Yale University (www.yale.edu)
Contact: michael^strickler_at_yale^edu