Dear Kay
You mean after convert .phs to .mtz ,use the .mtz file refine the initial
structure model? By the way , what's the difference between this density map
with the density map modified after phaser-EP density modification? Thanks a
lot!!!
Best Regard
Shijun
> -----原始邮件-----
> 发件人: "Kay Diederichs" <[email protected]>
> 发送时间: 2016年12月28日 星期三
> 收件人: [email protected]
> 抄送:
> 主题: Re: [ccp4bb] SAD phasing
>
> Dear Shijun,
>
> hkl2map is a very nice graphical user interface that makes it easy to use the
> SHELX programs; I've used it successfully around 3A. You find documentation
> and download information for SHELX C/D/E and hklmap in the CCP4 community
> wiki, at
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/SHELX_C/D/E
>
> hkl2map also writes a script, xxx_phs2mtz.csh
>
> #!/bin/csh -f
> #
> # Shell script for converting phs to mtz-format
> # This script was written by HKL2MAP 0.4.c-beta
> # f2mtz keeps order of columns
> # cad picks up things in a different order and then writes E1...E4
> #
> # To convert from phs to mtz type:
> # ./sad_phs2mtz.csh <name>.phs
> #
> set fname = $1:r
> f2mtz hklin ${fname}.phs hklout t_tmp.mtz > t_f2mtz.log <<END
> CELL 79.100 79.100 38.3 90 90 90
> SYMM P212121
> LABOUT H K L FP FOM PHIB SIGFP
> CTYPOUT H H H F W P Q
> END
> #
> cad hklin1 t_tmp.mtz hklout $fname.mtz > t_cad.log <<eof-cad
> LABIN FILE 1 E1=FP E2=SIGFP E3=PHIB E4=FOM
> LABOUT E1=FP E2=SIGFP E3=PHIB E4=FOM
> eof-cad
>
>
> that helps with the conversion of the .phs file to a .mtz file. The latter
> can then be used in the buccaneer/refmac autobuild/refine pipeline provided
> by ccp4i, to complete the structure.
> Please note that for the final refinement stages (which involve manual model
> adjustment), one should switch from this SHELXE-provided file to a .mtz file
> written by XDSCONV or (C)TRUNCATE because SHELXE does not use the
> French&Wilson procedure for converting intensities to amplitudes.
>
> Hope that helps,
>
> Kay
>
> On Wed, 28 Dec 2016 14:46:03 +0800, 张士军 <[email protected]> wrote:
>
> >Hello everyone
> >
> > I am learning phasing SAD data now ,and I got some files(like i.phs , .pdb
> > ,fa.res, fa.pdb) when I using SHELXC/D/E,and I know fa.pdb and fa.res
> > (which contain heavy atom information) are used for the further solution
> > searching ,and .phs file can read by coot. my question are :what is the
> > .phs used for(or which step it can be used ?) ,just for check my structure
> > ? Can I convert this .phs file into .mtz ,and used it for refinement or
> > model building after I found structure solution ? And only the heavy atom
> > site file (fa.pdb)is used when I searching my structure solution using
> > software? Can you guys give me some software suggestions about solution
> > searching after SHELXC/D/E when the data resolution is around 3A? Thanks a
> > lot !!!!
> >
> >Best Regard
> >
> >Shijun
