::!\bin\sh

::
:: Procedure  for finding water peaks. 
:: An atom map generated with SFALL is used to mask out the protein regions in
:: both an fo-fc and 2fo-fc map.  These solvent maps are then averaged and 
:: searched for peaks.  
::
:: fofcmap script does the same thing but only uses fo-fc map
::

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:: Generate atom map for final coordinates
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sfall MAPOUT %TEMPRES%\toxd_fc.map XYZIN %TOXD%\toxd.pdb < %SCRIPTWIN%\waterpeaks1.dat 

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:: Calculate sfs for final coordinates -
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sfall HKLIN %TOXD%\toxd.mtz HKLOUT %TEMPRES%\toxd.mtz  XYZIN %TOXD%\toxd.pdb < %SCRIPTWIN%\waterpeaks2.dat

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:: Fo-Fc map from final coordintes.  
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fft HKLIN %TEMPRES%\toxd.mtz  MAPOUT %TEMPRES%\toxd_fo-fc.map  < %SCRIPTWIN%\waterpeaks3.dat

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:: 2Fo -fc map from final coordintes.  
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fft HKLIN %TEMPRES%\toxd.mtz  MAPOUT %TEMPRES%\toxd_2fo-fc.map  < %SCRIPTWIN%\waterpeaks4.dat

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:: exclude points from 2fo-fc map which occur in fcalc map
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overlapmap MAPIN1 %TEMPRES%\toxd_fc.map  MAPIN2 %TEMPRES%\toxd_2fo-fc.map  MAPOUT %TEMPRES%\toxd_2fo-fc_masked.map  < %SCRIPTWIN%\waterpeaks5.dat

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:: exclude points from fo-fc map which occur in fcalc map
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overlapmap MAPIN1 %TEMPRES%\toxd_fc.map  MAPIN2 %TEMPRES%\toxd_fo-fc.map  MAPOUT %TEMPRES%\toxd_fo-fc_masked.map  < %SCRIPTWIN%\waterpeaks5.dat

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:: average 2 solvent maps now
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overlapmap MAPIN1  %TEMPRES%\toxd_fo-fc_masked.map MAPIN2  %TEMPRES%\toxd_2fo-fc_masked.map MAPOUT  %TEMPRES%\toxd_av_masked.map < %SCRIPTWIN%\waterpeaks6.dat

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:: run peakmax with electron density level 0.15  - look at 2fo-fc, fo-fc 
::                                                 to get sensible level
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::  run mapmask to cover molecule

mapmask XYZIN %TOXD%\toxd.pdb MAPIN  %TEMPRES%\toxd_av_masked.map MAPOUT  %TEMPRES%\toxd_av_masked.ext < %SCRIPTWIN%\waterpeaks7.dat

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::  Some peaks may appear twice since map has been extended.
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peakmax XYZOUT %TEMPRES%\toxd_peaks.pdb MAPIN  %TEMPRES%\toxd_av_masked.ext < %SCRIPTWIN%\waterpeaks8.dat

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:: run atpeak to check distances within 3.6A
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watpeak PEAKS %TEMPRES%\toxd_peaks.pdb XYZIN %TOXD%\toxd.pdb xyzout %TEMPRES%\toxd_waters.pdb < %SCRIPTWIN%\waterpeaks9.dat