Oh dear - I havent used SIGMAA for a long time .
If you use REFMAC to calculate your SFs then it generates FC PHIC and
FOM in the output. That is the easiset approach to getting started..
Isnt there a GUI task to do just this?
Eleanor
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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