Re: [ccp4bb]: Xtalview maps from Refmac5 in CCP4i

[Jason Maynes <jason@biochem.ualberta.ca>]

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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
*************************