One or two more comments.
There is a later paper by Andrew Leslie showing that the WANG real space
averaging can be carried out very simply and much faster in reciprocal
space - and this is the method used by all subsequent programs.
density modification using calculated phases is somewhat fraught - of
course the map will have strong density where there are atoms in the
model, regardless of whether they are in the right place or not. Using
FOM helps reduce this bias but it will still be there. It is most useful
when you only have a partial model..
Eleanor
there Hailiang Zhang wrote:
Hi,
I wanted to do solvent flattening for my map using Wang's method. I used
CCP4-DM, and now have several questions:
1. DM seems requiring the FOM, so I generated FOM using SIGMAA by
providing FP, FC and SIFFP using the following:
############################
sigmaa HKLIN in.mtz HKLOUT out-sigmaa.mtz << eof
title tt
labin FP=FP SIGFP=SIGFP FC=FC PHIC=PHIC
labout DELFWT=DELFWT FWT=FWT WCMB=WCMB
symmetry $spcgrp
END
eof
#############################
I think the output FOM should be in range between 0 to 1; however, it
produced FOM between -1 to 1 based on my in.mtz. This leads to complaints
by the following DM calculation, and I am not sure whether I could avoid
this.
2. My DM script is as follows:
#############################
dm HKLIN "./1KP8-NewSharpRescaleB0-sigmaa-oriB.mtz" HKLOUT
"./1KP8-NewSharpRescaleB0-sigmaa-oriB_dm.mtz"<<dmtest
mode -
SOLV -
NOHIST
combine PERT
scheme ALL
ncycles -
1
solc 0.6
solmask -
frac 0.6 -
0.4 -
radius 3.0 2
ncsmask
LABIN FP = FWT SIGFP = SIGFP PHIO = PHIC FOMO = WCMB
LABOUT FDM=FDM PHIDM=PHIDM FOMDM=FOMDM FCDM=FCDM PHICDM=PHICDM
END
dmtest
##############################
I am not sure whether there the above is ok for the purpose of a simple
real-space solvent flattening using Wang's method. By the way, my map is
at resolution 2.0, and I am not sure what is the best radius for this
resolution.
2. Based on Wang's paper (Wang, B. C. (1985) Methods in Enzymology 115,
90-112), the solvent flattening is carried out in real space, and since my
goal it simply modify my map, and I don't think I need FOM etc. So, can
CCP4 (or anyother packages like Phenix, CNS, UPPSALA...,) provide a simple
real-space solvent flattening without too much complications?
Thanks a lot for any hints.
Best Regards, Hailiang
