You can abuse/mis-use the TLSMD server from Ethan to analyse domain
movements and draw your conclusions accordingly, see here http://skuld.bmsc.washington.edu/~tlsmd/
Jürgen
On 7 Jan 2009, at 16:54, Jacob Keller wrote:
Dear Crystallographers,
I am sure that most here have dealt with the issue, when making
superpositions of conformationally-different structures, of which
regions to align as references and which to call "mobile."
Conformational changes can range from very local (e.g., unwinding of
a helix) to very diffuse (e.g., subtle but significant rigid body
shifts between two domains.) In the first case, it would probably
make sense to do a global least-squares fitting, but in the latter,
one would do better to fix one of the domains, and show the shift in
the other domain. These cases, however, presuppose that one knows
which type of case one is dealing with. This could be done by
guesswork and trial-and-error, but does anybody know of an approach
(e.g., a program) to define the most reasonable way to think about a
given conformational change? Variable-size sliding-window least-
squares superpositions with comparisons of local versus global
rmsd's come to mind, but I do not know whether this has been
implemented anywhere, and would not know readily how to set the
parameters thereof either.
Best Regards,
Jacob Keller
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.491.2438
cel: 773.608.9185
email: j-kell...@northwestern.edu
*******************************************
-
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Biochemistry and Molecular Biology, W8708
615 North Wolfe Street
Baltimore, MD 21205
Phone: +1-410-614-4742
