::!\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 :: :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: Generate atom map for final coordinates :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: sfall MAPOUT %TEMPRES%\toxd_fc.map XYZIN %TOXD%\toxd.pdb < %SCRIPTWIN%\waterpeaks1.dat :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: Calculate sfs for final coordinates - :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: sfall HKLIN %TOXD%\toxd.mtz HKLOUT %TEMPRES%\toxd.mtz XYZIN %TOXD%\toxd.pdb < %SCRIPTWIN%\waterpeaks2.dat :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: Fo-Fc map from final coordintes. :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: fft HKLIN %TEMPRES%\toxd.mtz MAPOUT %TEMPRES%\toxd_fo-fc.map < %SCRIPTWIN%\waterpeaks3.dat :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: 2Fo -fc map from final coordintes. :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: fft HKLIN %TEMPRES%\toxd.mtz MAPOUT %TEMPRES%\toxd_2fo-fc.map < %SCRIPTWIN%\waterpeaks4.dat :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: exclude points from 2fo-fc map which occur in fcalc map :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: overlapmap MAPIN1 %TEMPRES%\toxd_fc.map MAPIN2 %TEMPRES%\toxd_2fo-fc.map MAPOUT %TEMPRES%\toxd_2fo-fc_masked.map < %SCRIPTWIN%\waterpeaks5.dat :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: exclude points from fo-fc map which occur in fcalc map :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: overlapmap MAPIN1 %TEMPRES%\toxd_fc.map MAPIN2 %TEMPRES%\toxd_fo-fc.map MAPOUT %TEMPRES%\toxd_fo-fc_masked.map < %SCRIPTWIN%\waterpeaks5.dat :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: average 2 solvent maps now :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: overlapmap MAPIN1 %TEMPRES%\toxd_fo-fc_masked.map MAPIN2 %TEMPRES%\toxd_2fo-fc_masked.map MAPOUT %TEMPRES%\toxd_av_masked.map < %SCRIPTWIN%\waterpeaks6.dat :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: run peakmax with electron density level 0.15 - look at 2fo-fc, fo-fc :: to get sensible level :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: 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 :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: Some peaks may appear twice since map has been extended. :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: peakmax XYZOUT %TEMPRES%\toxd_peaks.pdb MAPIN %TEMPRES%\toxd_av_masked.ext < %SCRIPTWIN%\waterpeaks8.dat :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: :: run atpeak to check distances within 3.6A :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: watpeak PEAKS %TEMPRES%\toxd_peaks.pdb XYZIN %TOXD%\toxd.pdb xyzout %TEMPRES%\toxd_waters.pdb < %SCRIPTWIN%\waterpeaks9.dat