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
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