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

[Roberto Steiner <steiner@ysbl.york.ac.uk>]

***  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
>