%%%%%% New higher-throughput server for TLSMD analysis %%%%%%
http://skuld.bmsc.washington.edu/~tlsmd
We have upgraded the TLSMD web server, and invite you all to try it out.
The new server is faster, and can handle multiple jobs in parallel.
It does additional pre-screening of submitted files to spot potential
problems before they are run. If the pre-screening rejects an input
file that you think should have been accepted, please let us know.
In addition to generating input files for use with refmac, the new server
also produces multi-group TLS descriptions for use with PHENIX.refine.
Background summary of what the TLSMD server does
The TLSMD server creates a model for molecular flexibility based on a
refined protein (or RNA) crystal structure. The model is constructed
by breaking each protein chain into segments, and refining a TLS
(Translation/Libration/Screw) description for each segment.
This formalism allows one to describe with relatively few parameters
the anisotropic motions and microconformations of the crystalline
protein. In many cases it produces a much better description of the
crystal contents than a conventional model that tries to account for
these effects by assigning a single isotropic B factor for each atom.
Thus the TLSMD model often, although not always, yields better R and
Rfree values and improved electron density maps. Over and above that,
the component groups identified by TLSMD may yield insight into hinge
motions, local conformational flexibility, and other dynamic properties
of the protein relevant to its behaviour in solution as well as in the
crystal.
In essence, TLSMD takes a conventional model with individual atomic
B factors as input, and constructs a model that interprets those atomic
B factors as arising from the motion of larger groups. In the context
of the TLSMD server, you can think of the input B values as
observations ("B_obs"), and the predictions from the multi-group TLS
model as calculations ("B_pred"). The server helps you to choose a
multi-group model that does the best job of describing the distribution
of B factors in your input structural model. The TLSMD model parameters
themselves can then be further refined against your diffraction data
in either Refmac or PHENIX.refine.
More information, examples, and reprints of the papers describing
TLSMD are available through the front page of the TLSMD web site
http://skuld.bmsc.washington.edu/~tlsmd
--
Ethan A Merritt
Dept of Biochemistry
University of Washington - Seattle WA 98195-7742
