Dear Shijun, you can load the .phs file into coot and see the density; you don't need a .mtz file for this specific purpose.
However, e.g. buccaneer does not read the .phs file which is why you need to convert it. And "Use phi/fom instead of HL coefficients" in ccp4i. The density modification method of SHELXE is described in http://dx.doi.org/10.1107/S0907444909038360 ; the methods in the phaser-EP are different - references are at http://www.phaser.cimr.cam.ac.uk/index.php/Publications . best, Kay 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" <[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 > -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: [email protected] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box 647, D-78457 Konstanz
