Hi Intekhab Alam,
an Fobs-Fobs' map usually works only if the two crystals are
isomorphous, which means that there are neither large cell constant
changes nor any other larger structural changes (like overall rotations,
domain movements, other rearrangements) than the bound compound (ligand,
heavy atom, ...). Scaleit produces a plot of Riso against resolution
which ideally should resemble the scattering curve of the bound compound
(~ like an atomic scattering curve for instance), plus a mild increase
at high resolution due to the increasing noise component at higher
resolution. If the curve starts at high Riso values and increases
steeply, this would indicate anisomorphism, and there is probably no
chance to detect your compound signal.
All this is qualitative, but you could estimate the expected change with
the Crick-Magdoff equation by replacing the heavy atoms with a sum over
your compound atoms. The Crick-Magdoff equations has been recently
discussed on this board:
http://www.mail-archive.com/[email protected]/msg10039.html
Good luck,
Dirk.
Am 29.09.10 09:09, schrieb intekhab alam:
Hi Folks
I have a query regarding the difference map between the two structures
ligand bound data (2.5A) and native (2.8A).
I tried to calculate the fourier difference map between two data sets
ligand bound- native.
The protocol in CCP4 that i used is as:
1.merge the mtz file of native nad ligand bound using cad
2. scaling this combine file with scaleit program followed by map
generation uisng fft.
I got the map but i did not find the fu;ll map of the ligand,i can
only see small density nera the ligand binding site at 5 sigma level.
I have calculated omit map that cleraly showed the ligand.
why is such discrepency in the two cases, is there is something
missing from the calculation. kindly help me out.
Thanks and regards
Intekhab alam
--
INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
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Dirk Kostrewa
Gene Center Munich, A5.07
Department of Biochemistry
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: [email protected]
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