Hi Hailiang, Be sure to include "PARTIAL WCMB" in your sigmaa script. This option outputs something more like a conventional FOM for use in DM.
Also, I would allow DM to run more cycles and suggest starting with default parameters for solvent masking and density levels and then looking at the resulting maps. You have also specified ncsmask parameters without specifying ncs or asking the program to utilize ncs. Try the CCP4i GUI, it avoids many of these technical problems. Best, --Paul --- On Wed, 6/2/10, Hailiang Zhang <zhan...@umbc.edu> wrote: > From: Hailiang Zhang <zhan...@umbc.edu> > Subject: [ccp4bb] About solvent flattening > To: CCP4BB@JISCMAIL.AC.UK > Date: Wednesday, June 2, 2010, 3:04 PM > 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 >
