EPMR (now Open-EPMR, http://www.epmr.info) is an excellent alternative
for finding difficult, high-dimensional MR solutions. Experiment with
various resolution limits. We solved an asymmetric unit with 3
difficult-to-place dimers of low sequence homology by gradually
increasing the high-resolution limit of the structure factor data used.
If you have a partial static solution, it can look for additional
protein chain placements. It is strongly recommended for your type of
problem that you set the correlation coefficient threshold for a good
solution to 1.00 and not use the defaults. This will force EPMR to do an
exhaustive search.
Cheers,
--
------------------------------------------------------------------------
Roger S. Rowlett
Professor
Colgate University Presidential Scholar
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: [EMAIL PROTECTED]
Lucas Bleicher wrote:
I've had a very good experience with MrBump:
http://www.ccp4.ac.uk/MrBUMP/
Not only because of the program itself, which was able
to find an unexpected template for the problematic
chain (the first one was straightforward in Phaser),
but also because of great support from Martyn & Ron.
It's definitely worth a try.
Lucas
--- Anjali Mehta <[EMAIL PROTECTED]> escreveu:
Dear All,
I am working with a Bifunctional protein of
molecular weight ~60 kDa.
I have a 3.3 angstrom native dataset. The matthews
number show there are 6
molecules in the asymmetric unit.
The structures of the individual domains are already
known from prokaryotes.
The sequence identity with the known structures are
about 30%.
I have tried molecular replacement using the two
parts as models
respectively with CNS, MOLREP, PHASER etc. However I
always get the solution
for one domain. I have also tried to fix that domain
and find the other one.
But none of the programs can find a solution.
I am trying to model build the correct sequence of
one domain using a
density modified (using CNS), NCS averaged (using
RAVE) map but the map does
not look very good. The side chains are not clear.
That might be due to the
fact that I am only having a partial model.
Any suggestion will be appreciated.
Thanks.
Ms. Anjali Mehta
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