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You can also run origins.com from ELVES and it will take care of your
problem.
You can find the standalone script here: (for 1200aa it takes about 90
seconds on my computer, but that depends on your space group)
http://ucxray.berkeley.edu/~jamesh/elves/goodies.html
Rerun a rigid body refinement and you're ready to go.
If you only want to compare two deposited structures e.g. to see if the
ligand would fit your coordinates, then just SSM superimpose with coot
or EBI SSM or any other tool.
Juergen
Shane Atwell wrote:
When solving structures that are the same crystal form as a parent,
what's the best way of getting or moving the solution to the same
position as the parent? This is for cases where a typical rigid body
refinement isn't sufficient to pull out the solution.
It is not very convenient to look at the parent and the solution and
then fix the solution using pdbset symgen, at least for dozens or
hundreds of structures.
I've tried using beast to do the MR in a small box around the parent
solution, and it works, but takes a long time even for a 'small'
search area (e.g. 10 degrees and 2 Angstroms).
Its possible that doing the rigid body refinement w/ lower res data
could pull in solutions that are further off, but I doubt it would be
very robust..
It also seems possible to use contact or a similar program to find
which symmetry molecule of the solution 'clashes' with the parent
solution. I'm toying with this, but haven't gotten it to work yet.
Short of custom modification of the MR program, is there something
available that I'm missing?
Shane Atwell
--
Jürgen Bosch
Howard Hughes Medical Institute and
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
