I'm not quite clear what your aim is here, but if you want to reproduce
Wan'g method exactly, DM can't do it as it has a whole lot of more
recent stuff built in (gamma correction, masking algorithms etc).
If you really want to implement Wang's method (and I'm not sure quite
why you would, because density modification has come a long way since
then), then I think you're going to have to do it stepwise.
- fft or cfft can calculate the map.
- sfall or cinvfft can calculate structure factors from the modified map.
- sigmaa or csigmaa can calculate weights from the modified structure
factors (although if I remember correctly Wang used Sim rather than
Sigmaa weighting - not sure if there is a program that will still do that).
- modifying the map can be done with mapmask.
- calculating the mask - tricky. Multiple runs of mapmask, fft and
sfall will do it I think. Or you could use solomon, but that uses a
different masking algorithm.
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
