Dear Bruno,
Thank you very much for your quick response!
I've managed to generate mtz file (I've only needed to add "set
spacegroup P1" while running sftools).
However, the problem remains.
I am not sure if this is the case but Phenix reads columns 1 and 2 as
"Map coefs".
Do you have any clue?
Best regards,
Wojtek
On 07/13/2012 05:53 PM, Bruno KLAHOLZ wrote:
Dear Wojtek,
you can try something of this type to get the EM map converted into an hkl list
and mtz file with I's and some sigma I's estimated to 1/10 of the I's (the
latter is required for running fittings/refinements etc.).
Best,
Bruno
/usr/local/rave/rave_linux/lx_mapman<<EOF
re m2 name_40-8A.ccp4 ccp4
no m2
uvw
m2
3
1
2
write m2 name_40-8A-uvw.ccp4 ccp4
quit
EOF
/usr/local/ccp4-version/bin/sftools<<EOF
MAPIN name_40-8A-uvw.ccp4 map
MAP2SF
calc q col sigma = col 1 10 /
CALC I col test = rfree(0.05)
WRITE name_40-8A-uvw.fobs col 1 3 2 4
xpl
FOBS
PHASE
write
name_40-8A-uvw.mtz
quit
-----Message d'origine-----
De : CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] De la part de Wojtek
Potrzebowski
Envoyé : Friday, July 13, 2012 5:28 PM
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] Rigid body refinement with phenix using EM maps.
Dear all,
I want to refine a model of the complex that consists of rigid subunits using
an electron microscopy electron density map.
I've tried to use phenix for this purpose. Thus I have to back-FT the electron
density map to a mtz reflection file.
I've experienced problem using sfall for this purpose, but cinvfft has done a
job (I can read a resulting file with mtzdmp).
However phenix doesn't read this file properly (data labels box is empty).
Can anyone help me on this, please?
I am looking forward to hearing from you, Wojtek
###########################################################################
Dr. Bruno P. Klaholz
Department of Integrated Structural Biology
Institute of Genetics and of Molecular and Cellular Biology
IGBMC - UMR 7104 - U 964
1, rue Laurent Fries
BP 10142
67404 ILLKIRCH CEDEX
FRANCE
http://www.igbmc.fr/
http://igbmc.fr/Klaholz
