Hi Ivan,
two ways (at least) to do it in PHENIX:
- phenix.refine always computes anomalous difference Fourier map
(provided that your input data file contains Fobs(+) and Fobs(-)). The
command below will do it:
phenix.refine model.pdb data.mtz strategy=none
main.number_of_macro_cycles=0 output.prefix=maps_only
- you can use phenix.maps that is a general tool to compute a broad
variety of maps. Type "phenix.maps" from the command line for usage
instructions. You need to have the latest development (or one of) PHENIX
nightly build for this.
All this is available from the GUI too.
Pavel.
On 2/18/10 3:34 PM, xaravich ivan wrote:
Hello,
I wanted to make an anomalous difference fourier map of a structure
with zinc bound to it. However I have not been successful in making
the map and I would really appreciate your help if anyone could
suggest me where I am going wrong.
I solved this zinc bound structure, by molecular replacement from a
calcium bound structure (1.4 angstrom) that I solved. I want to show
that the zinc binds to the identical site by the anomalous difference
fourier map.
I am using CCP4i and the steps that I have been taking are, (names of
the files are arbitrary)
1) generating structure factors and phases from the solved coordinates
by SFALL
Input files
zinc bound pdb
original zinc .mtz data from synchrotron
output file
XXXXsfall.mtz
2)merging the XXXXsfall.mtz containing the PHICalc and FCalc columns
with the original synchrotron .mtz file containing DANO and SIGDANO by
running CAD.
input files
XXXXsfall.mtz and zinc synchrtron .mtz
output file
CAD.mtz
3) Running FFT to make anomalous map, selecting labels from CAD.mtz as
input files.
There is an output map file but nothing in it. all the values are 0
and the map is not recognized by coot. There is no error message in
the log file.
I must be missing something or doing something wrong/stupid.
Thanks,
Ivan
