Dear Shijun,

You can find a lot of information about these programs on the SHELX 
homepage, now moved to
shelx.uni-goettingen.de  See in particular the sections "Tutorials & 
talks" and "SHELX Workshops".
Converting the .phs file to .mtz is not needed for looking at the map  
(Coot can read .phs directly),
and is not recommended for refinement. If you convert .phs to .mtz and 
use that for refinement,
if you are not careful the resolution for the refinement may then be 
much better that you actually
measured,  because you are refining against the "free lunch" 
resolution-extended data.

Best wishes, George Sheldrick



On 28.12.2016 11:43, 张士军 wrote:
> 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" <[log in to unmask]>
>> 发送时间: 2016年12月28日 星期三
>> 收件人: [log in to unmask]
>> 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 <[log in to unmask]> 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


-- 
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582