Re: [ccp4bb] About solvent flattening

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: RES: Off-topic: hollow protein crystals
From: Andre Ambrosio andre {- dot -} ambrosio {- at -} CEBIME {- dot -} ORG {- dot -} BR
Date: 2010-06-03

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Subject: Re: About solvent flattening
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-06-03

Subject: Re: About solvent flattening
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-06-03

One or two more comments.

There is a later paper by Andrew Leslie showing that the WANG real space
averaging can be carried out very simply and much faster in reciprocal
space - and this is the method used by all subsequent programs.

density modification using calculated phases is somewhat fraught - of
course the map will have strong density where there are atoms in the
model, regardless of whether they are in the right place or not. Using
FOM helps reduce this bias but it will still be there. It is most useful
when you only have a partial model..

Eleanor

there 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"<
> 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

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: RES: Off-topic: hollow protein crystals
From: Andre Ambrosio andre {- dot -} ambrosio {- at -} CEBIME {- dot -} ORG {- dot -} BR
Date: 2010-06-03

Next message:
Subject: Re: About solvent flattening
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2010-06-03