Re: [ccp4bb] About solvent flattening

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

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Subject: Displaying repeats in a amino acid sequence
From: Klaus Sengstack sengstack-klaus {- at -} YAHOO {- dot -} DE
Date: 2010-06-04

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Subject: Re: Displaying repeats in a amino acid sequence
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2010-06-04

Subject: Re: About solvent flattening
From: Bi-Cheng Wang wang {- at -} BCL1 {- dot -} BMB {- dot -} UGA {- dot -} EDU
Date: 2010-06-04

Hi Hailiang,

My original ISAS program has been incorporated in the SGXPro program
suite (Fu, Rose and Wang, 2005, Acta Cryst. D61, 951) and is currently
used with other phasing programs in SGXPro at SER-CAT. You may find
the description on the use of SGXPro by accessing the SER-CAT website
at www.ser-cat.org, then click "Beamline User's Guide" ==> "Novel
Structure Solution". For questions on how to access SGXPro, you may
contact Zheng-Qing (Albert) Fu by clicking "About SER-CAT" ==> Staff
==> Albert.

SGXPro is a parallel workflow engine that was designed to
automatically manage communication between the different processes and
build systematic searches of algorithm/program/parameter space to
generate the best possible result for a given data set. There were a
number of cases when we were happily surprised that this 25-year old
ISAS program was actually selected as the best choice by SGXPro for
phasing some new data sets. We do not have an explanation on why the
ISAS program works well on these particular data sets, but we are
documenting the cases closely. Albert also routinely uses the ISAS
program for determining the handedness of the heavy atom (anomalous
scatterer) site as it works quite well automatically.

With best wishes,

B.C.

On Jun 2, 2010, at 3:04 PM, 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: Displaying repeats in a amino acid sequence
From: Klaus Sengstack sengstack-klaus {- at -} YAHOO {- dot -} DE
Date: 2010-06-04

Next message:
Subject: Re: Displaying repeats in a amino acid sequence
From: Tim Gruene tg {- at -} SHELX {- dot -} UNI-AC {- dot -} GWDG {- dot -} DE
Date: 2010-06-04