[buster-discuss] New BUSTER/TNT installation - seems to be almost working...

Thu Dec 14 07:41:51 GMT 2006

Hi Steve,

there is one limitation of the currently distributed BUSTER-TNT
version: it requires a CCP4 4.X installation (has to do with the way
MTZ headers changed between 4.X and 5.X). So you'll need to
install/use CCP4 4.2.2 with BUSTER-TNT.

The easiest way of getting a CCP4 4.2.2 installation is:

  1. go to 

      http://www.globalphasing.com/people/vonrhein/ccp4/index.html

     and download the ccp4_cv.sh script into an empty directory. Then
     run the script (in an environment where no other CCP4-related
     variables are set) to compile a 4.2.2 version:

      % chmod +x ./ccp4_cv.sh
      % ./ccp4_cv.sh -v 4.2.2

     Alternatively, you could try the pre-compiled binaries from

      ftp://ftp.ccp4.ac.uk/ccp4/4.2.2/binaries/README.html

  2. After that you'll need to tell BUSTER-TNT about the new 4.2.2
     installation: edit the file(s) $BDG_home/machines/*/ccp4.setup to
     point to this 4.2.2 installation.

  3. If you have any files with names busterfiles/datafiles/*.mtzlog
     you should remove them.

  4. if you have MTZ files from newer versions of CCP4, then you need
     to 'convert' them into CCP4 4.X MTZ files (re-write the header). You
     should be able to do this with the attached script (while sitting
     in the CCP4 4.X environment)

Then try again.

Sorry about this 'ancient' requirement for CCP4 4.X - the next release
will (obviously) work with later CCP4 versions (and MTZ files) too.

Cheers

Clemens

On Wed, Dec 13, 2006 at 07:29:54PM -0800, Steve Lane wrote:
> Greetings.  I have installed SHARP several times with success, but this
> is my first go at BUSTER.  Everything seems fine until I try to use
> (any) one of the sample data sets, at which point I get:
> 
> 
> ERROR in /usr/local/buster/buffet/cgi-bin/inputform.cgi
> 
>     The following return values are set:
> 
>     * Child error = 0
>     * OS error =
>     * Eval error = 0 
> 
> Error message  :   Error parsing the mtzdump output of /usr/local/buster/users/drsteve/None.buster/datafiles/Barnase.mtz Cell/symmetry/resolution information is missing 
> 
> 
> (Above this, on the same webpage, listed under "2. Diffraction Data",
> I see several function definitions, included below.)
> 
> Note that it doesn't seem to matter which dataset I use, the problem
> is always with Barnase.mtz.  It also doesn't *seem* to be a permissions
> problem - I was able to create ~/busterfiles without any problems, and
> I manually opened up the permissions on all the files and directories
> in ~/busterfiles (to 777) without any improvement.
> 
> Any help will be most appreciated.
> 
> --
> Steve Lane
> System, Network and Security Administrator
> Doudna Lab
> Biomolecular Structure and Mechanism Group
> UC Berkeley
> 
> ========================================
> 
> 2.    Diffraction data
>    function changeResol( type ) { var el; var defVal; var low_bound; var high_bound; if( type == 0 ) { el = document.launch.res_low.value * 1.0; defVal = file.reslo.value * 1.0; low_bound = document.launch.res_hi.value * 1.0; high_bound = file.reslo.value * 1.0; } else { el = document.launch.res_hi.value * 1.0; defVal = file.reshi.value * 1.0; low_bound = file.reshi.value * 1.0; high_bound = document.launch.res_low.value * 1.0; } checkBounds( el, 0.99*low_bound, 1.01*high_bound, defVal ); if( type == 0 ) { document.launch.le1.value = el; document.launch.bs1.value = el; document.launch.dn1.value = el; } else { document.launch.le2.value = el; document.launch.bs2.value = el; document.launch.dn2.value = el; } } function checkBounds( el, low_bound, high_bound, default_val ) { var value = el.value * 1.0; var low = low_bound * 1.0; var high = high_bound * 1.0; if( value < low || value > high ) { alert( "This value " + value + " must be between " + low + " and " + high ); el.value = default_val * 1.0; } } function Label( name, type ) { this.name = name; this.type = type; } function MTZ( name, cell, symm, res, labels ) { this.name = name; this.cell = cell; this.symm = symm; this.reslo = res[0] * 1.0; this.reshi = res[1] * 1.0; this.labels = labels; } function selectMTZ( f, selection ) { // Loop over all available MTZ files for( var i = 0; i < mtzs.length; ++i ) { if( mtzs[i].name == selection ) { file = mtzs[i]; f.res_low.value = file.reslo * 1.0; f.res_hi.value = file.reshi * 1.0; changeResol( 0 ); changeResol( 1 ); f.a.value = file.cell[0] * 1.0; f.b.value = file.cell[1] * 1.0; f.c.value = file.cell[2] * 1.0; f.alpha.value = file.cell[3] * 1.0; f.beta.value = file.cell[4] * 1.0; f.gamma.value = file.cell[5] * 1.0; f.symm.value = file.symm; document.launch.FP_Label.options.length = 0; var k = 0; for( var j = 0; j < mtzs[i].labels.length; ++j ) if( mtzs[i].labels[j].type == "F" ) ++k; --k; if( k > 0 ) { document.launch.FP_Label.options[0] = new Option( "None", "None", true, true ); document.launch.FP_Label.selectedIndex = 0; k = 1; } for( var j = 0; j < mtzs[i].labels.length; ++j ) { if( mtzs[i].labels[j].type == "F" ) { var selected = false; if( k == 0 ) selected = true; f.FP_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name, selected, selected ); ++k; } } document.launch.FP_Label.options[0].selected = true; document.launch.SIGFP_Label.options.length = 0; k = 0; for( var j = 0; j < mtzs[i].labels.length; ++j ) if( mtzs[i].labels[j].type == "Q" ) ++k; --k; if( k > 0 ) { document.launch.SIGFP_Label.options[0] = new Option( "None", "None", true, true ); document.launch.SIGFP_Label.selectedIndex = 0; k = 1; } for( var j = 0; j < mtzs[i].labels.length; ++j ) { if( mtzs[i].labels[j].type == "Q" ) { var selected = false; if( k == 0 ) selected = true; f.SIGFP_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name, selected, selected ); ++k; } } document.launch.SIGFP_Label.options[0].selected = true; document.launch.FreeR_flag_Label.options.length = 0; k = 0; for( var j = 0; j < mtzs[i].labels.length; ++j ) if( mtzs[i].labels[j].type == "I" ) ++k; --k; if( k > 0 ) { document.launch.FreeR_flag_Label.options[0] = new Option( "None", "None", true, true ); document.launch.FreeR_flag_Label.selectedIndex = 0; k = 1; } for( var j = 0; j < mtzs[i].labels.length; ++j ) { if( mtzs[i].labels[j].type == "I" ) { var selected = false; if( k == 0 ) selected = true; f.FreeR_flag_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name, selected, selected ); ++k; } } document.launch.FreeR_flag_Label.options[0].selected = true; document.launch.HLA_Label.options.length = 0; document.launch.HLB_Label.options.length = 0; document.launch.HLC_Label.options.length = 0; document.launch.HLD_Label.options.length = 0; f.HLA_Label.options[0] = new Option( "None", "None" ); f.HLB_Label.options[0] = new Option( "None", "None" ); f.HLC_Label.options[0] = new Option( "None", "None" ); f.HLD_Label.options[0] = new Option( "None", "None" ); k = 1; for( var j = 0; j < mtzs[i].labels.length; ++j ) { if( mtzs[i].labels[j].type == "A" ) { if( mtzs[i].labels[j].type == "HLA" ) f.HLA_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name, true, true ); else f.HLA_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name ); if( mtzs[i].labels[j].type == "HLB" ) f.HLB_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name, true, true ); else f.HLB_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name ); if( mtzs[i].labels[j].type == "HLC" ) f.HLC_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name, true, true ); else f.HLC_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name ); if( mtzs[i].labels[j].type == "HLD" ) f.HLD_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name, true, true ); else f.HLD_Label.options[k] = new Option( mtzs[i].labels[j].name, mtzs[i].labels[j].name ); ++k; } } break; } } } function clearHL( f, el ) { if( el.selectedIndex == 0 ) { f.HLA_Label.selectedIndex = 0; f.HLB_Label.selectedIndex = 0; f.HLC_Label.selectedIndex = 0; f.HLD_Label.selectedIndex = 0; } } var mtzs = new Array( 4 );
> 
> 
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> 

-- 

***************************************************************
* Clemens Vonrhein, Ph.D.     vonrhein AT GlobalPhasing DOT com
*
*  Global Phasing Ltd.
*  Sheraton House, Castle Park 
*  Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group      (http://www.globalphasing.com)
***************************************************************
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[buster-discuss] New BUSTER/TNT installation - seems to be *almost* working...

[buster-discuss] New BUSTER/TNT installation - seems to be almost working...