On Apr 4 2008, hari jayaram wrote:
Hi everyone, I have a phaser molecular replacement solution for my
membrane protein which crystallized in spacegroup P3. The diffraction
data is good to about 3.3 A. The model I used had 39% homology to the
given protein. A solvent content analysis suggests that there probably
are three dimers in the ASU ( to give about 67% solvent) Phaser
sucessfuly found two dimers in the ASU with good density and a third
dimer with very weak almost "non-existent" density. I am now trying to do
some NCS-averaging using DM to see If I can improve the desnity for dimer
3 and have a question about the different co-efficients I should be using
for the averaging DM run.
Question1:
The phaser output mtz file has a PHWT and a PHIC . For carrying out DM with
flattening, averaging and histogram matching which phases do I use PHIC or
PHWT along with observed Fo. Also for the weight do I use the FOM.
Question2:
The output mtz from DM run either way above , now has a PHIDM and a PHWT
along with a FWT and FC. Which coefficients should I be using to get a map
after DM for building.
FWT and PHWT
or
Fo and PHIDM
or
FWT and PHIDM.
Thank you for your help
Hari
In the MTZ file produced by Phaser, the FWT/PHWT pair provide the 2mFo-DFc
map coefficients that should reduce model bias. I'd suggest starting DM
from these coefficients, which you can do by adding "FDM=FWT PHIDM=PHWT" to
the LABIN command for DM. (If you want to do this from the current ccp4i
GUI for DM, the only way is to use the Run&View Com File command.)
After running DM, the map coefficients to view in coot are FDM/PHIDM.
Good luck!
Randy Read
