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Re: [ccp4bb]: Xtalview maps from Refmac5 in CCP4i
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*** CCP4 home page http://www.ccp4.ac.uk ***
Crossed-wires I'm afraid. As we discussed at the time, I was unable
to reproduce your problem. With hindsight, it looks like this
was because Pete had fixed Roberto's problem, and I failed to
notice what Pete was doing. Apologies for that.
Anyway, the fix is in 4.2.1 So regarding the original posting, either
you are not really using 4.2.1 or it is a different problem. Can you
double check please?
Cheers
Martyn
> Hello:
>
> I reported the problem too but they weren't generous enough to supply a
> script or even tell me what the problem was (although my phases weren't
> zero but it did look like it used the wrong cell). I was just using
> sftools to create a phs file from the mtz, which works as well.
>
> Cheers,
> JTM
>
> *************************
> Jason Thomas Maynes
> MD/PhD Program
> Faculty of Medicine
> University of Alberta
> jason@biochem.ualberta.ca
> *************************
>
> On Thu, 25 Jul 2002, Roberto Steiner wrote:
>
> > *** For details on how to be removed from this list visit the ***
> > *** CCP4 home page http://www.ccp4.ac.uk ***
> >
> > On Thursday 25 Jul 2002 8:51 am, Francisco J. Enguita wrote:
> > > *** For details on how to be removed from this list visit the ***
> > > *** CCP4 home page http://www.ccp4.ac.uk ***
> > >
> > > Dear all :
> > >
> > > I've got some problems when running Refmac5 from the ccp4i interface in
> > > the 4.2.1 version. When I select FWT and DELFTW maps output in Xtalview
> > > format, the electronic density is not placed in the refined model (it
> > > looks like the maps were calculated using a different cell dimensions
> > > and/or spacegroup). However, when the selected output format for the
> > > maps was CCP4, and the maps were converted to Xtalview format by using
> > > the MAP2FS utility, everything was correct.
> > >
> > > Has anybody experienced a problem like this ?. Any help will be
> > > wellcome.
> > >
> > > Cheers
> > >
> > > Francisco
> > >
> >
> > Hi Francisco,
> >
> > I suspect your problem is in the .phs files generated by the script
> > refmac_maps.script which lives in $CCP4/ccp4i/scripts. Most likely all your
> > phases are zero!
> > I reported the problem to ccp4 people (I guess they're planning to fix the
> > problem for the next release) and I got immediately a replacement script
> > which works fine. Try to replace the old scipt whith the following one and
> > see how things go.
> >
> > Cheers,
> > Roberto
> >
> > ---------------------------------------------------------------------------
> > # Create refmac-specific maps
> > # This script is used independently or sourced from refmac script
> > #
> >
> > source [SearchPath TOP utils map_utils.tcl]
> >
> > if { ![info exists MAPOUT1] || $MAPOUT1 == "" } {
> > set mapout_1 [SetOutputFileRoot -map]_FWT.map
> > } else {
> > set mapout_1 $MAPOUT1
> > }
> > if { ![info exists MAPOUT2] || $MAPOUT2 == "" } {
> > set mapout_2 [SetOutputFileRoot -map]_DELFWT.map
> > } else {
> > set mapout_2 $MAPOUT2
> > }
> >
> >
> > if { $EXTEND_MAP } {
> > CreateMap $MAPOUT_FORMAT $HKLOUT mapout_1 "2FO-1FC" \
> > [list F1 PHI ] [list $FWT $PHWT] \
> > -cover $XYZOUT $MAP_BORDER
> > CreateMap $MAPOUT_FORMAT $HKLOUT mapout_2 "1FO-1FC" \
> > [list F1 PHI ] [list $DELFWT $PHDELWT] \
> > -cover $XYZOUT $MAP_BORDER
> > } else {
> > CreateMap $MAPOUT_FORMAT $HKLOUT mapout_1 "2FO-1FC" \
> > [list F1 PHI ] [list $FWT $PHWT]
> > CreateMap $MAPOUT_FORMAT $HKLOUT mapout_2 "1FO-1FC" \
> > [list F1 PHI ] [list $DELFWT $PHDELWT]
> > }
> >
> > AddOutputFile $mapout_1 MAP_DEFAULT $mapout_2 MAP_DEFAULT
> >
> > switch $MAPOUT_FORMAT \
> > O {
> > set macro_file [SetOutputFileRoot]_refmac_omap.mac
> > MakeOMapMacro $macro_file [list $mapout_1 $mapout_2 $mapout_2 ] \
> > [list 2fo pos neg ] [list 1.0 2.0 -2.0] \
> > [ list slate_blue red green ] 20.0
> > AddOutputFile $macro_file PROJECT
> > } XtalView {
> >
> > set crystal_file [SetOutputFileRoot]_refmac.xtal
> > set macro_file [SetOutputFileRoot]_refmac_xtal.script
> >
> > MakeXtalMacro $HKLOUT $crystal_file $macro_file \
> > [list $mapout_1 $mapout_2] [list Fo Fo ] [list 8 8 ]
> >
> > AddOutputFile $crystal_file PROJECT $macro_file PROJECT
> > }
> > ------------------------------------------------------------------------------------------------
> >
> > --
> > Roberto A. Steiner
> > York Structural Biology Lab, Department of Chemistry
> > University of York, Heslington, York, YO10 5DD, U.K.
> > Tel: (+44) 1904 434531
> > Fax: (+44) 1904 410519
> > >
> >
> >
> >
>
> *************************
> Jason Thomas Maynes
> MD/PhD Program
> Faculty of Medicine
> University of Alberta
> jason@biochem.ualberta.ca
> *************************
>
>
--
**************************************************************************
* *
* Dr. Martyn Winn *
* *
* Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, ENGLAND *
* Tel: +44 1925 603455 E-mail: m.d.winn@ccp4.ac.uk (personal) *
* Fax: +44 1925 603825 E-mail: ccp4@ccp4.ac.uk (CCP4 problems) *
* URL: http://www.ccp4.ac.uk/martyn/martyn.html *
**************************************************************************