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Hi,
After a long delay I just wanted to thank all those who replied to my
query about placing a large molecular fragment in electron density.
In fact I was already on the right path using MOLREP, but the problem
is that, as far as I can tell, the MOLREP output gives no indication
that it is using phased rotation and translation functions rather
than the traditional ones. Thus if the initial RF seems to have poor
S/N it is easy to believe that you have given the wrong input. Also
the documentation is not easy to understand on the subject of input
files. I made a CIF file with only one structure factor and one phase
(the original output was from SHARP, with several such columns) and
that did the trick. The R-factor was very poor but the solution was
unique and fit the density.
Cheers
Derek
On Oct 4, 2006, at 23:09, Peter Adrian Meyer wrote:
Hi,
fffear should work for this, assuming that your fragment is reasonably
well-ordered in your crystal (it'll probably work on the experimental
phases before solvent flattening if this is the case).
However, it expects inputs in terms of amplitudes and phases, so
you'll
either have to use your reflection data or back-transform the map.
Pete
Dear all,
Short of the painful process of moving it by hand, what is the
currently most efficient way to place a large protein fragment (say
350 amino acids) in an experimentally phased electron density map?
The resolution is 2.7Å and we can see some secondary structure
elements in the map.
Thanks
Derek
--
Derek Logan tel: +46 46 222 1443
Associate professor fax: +46 46 222 4692
Molecular Biophysics
Lund University
Box 124, Lund, Sweden
Pete Meyer
Fu Lab
BMCB grad student
Cornell University
