Sorry, a better command line for running SHELXE in this case would have
been:
shelxe name name_fa -a5 -s0.5 -q -h -z
this ensures that the heavy atoms are refined before calculating the
initial phases, this often gives
much better maps. If you are not sure whether the space group is P6122
or P6522, then you should
run shelxe twice, once with and once without -i (which would invert the
space group and atom
coordinates). It is usually worth trying different solvent contents (-s).
George
On 03/15/2013 11:09 AM, George Sheldrick wrote:
Dear Wei,
There is a new SHELX homepage with extensive documentation and downloading
instructions at: http://shelx.uni-ac.gwdg.de/SHELX/
SHELXE requires reflection files name.hkl (native) and name_fa.hkl
(data for phasing) and
and the heavy atoms in SHELX format in name_fa.res. I recommend
running SHELXC to prepare
the files and SHELXD to find the heavy atoms, then everything will be
in the right format. You can
either run the programs from the command line or use a GUI such as
hkl2map.
If (as it seems) your heavy atoms come from an isomorphous structure,
then you can run SHELXC
to read XDS_ASCII.HKL or .sca files to make the .hkl, files followed
by AnoDe (also part of SHELX) to
read name_fa.hkl and name.ent (your original full PDB file, no just
the heavy atoms) to make
name_fa.res containing the heavy atom sites from the anomalous map.
Then you have the files
you need to run SHELXE, e.g.
shelxe name name_fa -a5 -s0.5 -q
but see the documentation for more information about the command line
switches, e.g. -n for NCS.
The advantage of this is that your final structure will be relative to
the same origin as your original
PDB file.
Best wishes, George
On 03/15/2013 10:13 AM, Wei Feng wrote:
Dear all,
I have an original sca file with anomalous signal and a heavy atoms
sites file in PDB format.
PDB FILE :
CRYST1 77.780 77.780 187.640 90.00 90.00 120.00 P 61 2 2
SCALE1 0.012857 0.007423 -0.000000 -0.00000
SCALE2 -0.000000 0.014846 -0.000000 0.00000
SCALE3 0.000000 -0.000000 0.005329 -0.00000
ATOM 1 S HAT 1 -62.495 123.694 12.804 0.36 20.00 S
ATOM 9 S HAT 9 -49.984 90.531 2.130 0.32 20.00 S
ATOM 10 S HAT 10 -59.282 106.437 9.760 0.74 20.00 S
ATOM 84 S HAT 84 -60.153 114.024 15.399 0.52 20.00 S
... ...
Can I use SHELXE to perform phasing and density modification? How to
do it?
Thank you for your help!
Wei
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582