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Hi Michael,
you could try to use the morph server http://www.molmovdb.org/morph/
(you can also download the script if you want to do it locally on your
computer for privacy issues). Then you would have an idea which parts
move. I would use a monomer in each of your cases first before going to
higher numbers. You will also have to check which changes are due to
crystal contacts. Is there any part of your protein, which seems to
stay stable ? If yes, then you could use ccp4mg and define those parts
for superposition - alternatively you could do this also with LSQMAN by
hand :-)
A distance plot per residue should result in what you would like to add
to the B-value column, then you can use Rasmol etc. to colour by B-values.
Good luck,
Juergen
Michael Hothorn wrote:
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Dear list members,
I have solved a small proteins structure in seven different crystal forms.
These forms show very different symmetry, contain between 1 and 4 mols/AU and
cover a wide pH range. I would like to know, whether there are significant
structural changes. Currently, I have superimposed all molecules from all
different crystal forms onto one reference molecule by hand. Is there a piece
of software that does this analysis in a bit more clever way (e.g. taking into
account resolution, refinement statistics, crystal packing)? I heared about
ESCET from Thomas Schneider, but so far I could not try it out. In the end, I
would like to present a figure that shows rigid structural parts in blue and
flexible parts in red (e.g. via some value in the B-factor column).
any suggestions or comments ?
thank you!
Michael Hothorn
Structural & Computational Biology Programme
European Molecular Biology Laboratory (EMBL)
Meyerhofstrasse 1
69117 Heidelberg
Tel: 0049(0)6221 387 268 (office)
Tel: 0049(0)6221 387 609 (lab)
http://www.hothorn.de
--
Jürgen Bosch
Howard Hughes Medical Institute and
University of Washington
Dept. of Biochemistry, K-418
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4542
FAX: +1-206-685-7002
