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
