#!/bin/csh -f # # #--- check-----> cyc141 d13w #--- check-----> cyc20 rs1 # # shouldnt have any disorder atoms in files- # should select only one pair of conformations - label normal # but keep occupancy = 0.5 # # 1. Get temp files # # (i) get headers # grep CRYSTL ../brk/d13w_cyc141.brk > d13w.head grep SCALE ../brk/d13w_cyc141.brk >> d13w.head grep CRYSTL ../brk/rs1_cyc20.brk > rs1.head grep SCALE ../brk/rs1_cyc20.brk >> rs1.head # # (ii) Remove disorder atoms # the awk script - removes B atoms in disorder # changes A to space in disorder # conformation # /bin/awk -f ${CETC}/disorder.awk < ../brk/d13w_cyc141.brk \ > d13w_H.disorder_out # # (iii) get H chain # grep " H " d13w_H.disorder_out > d13w.H # # /bin/awk -f ${CETC}/disorder.awk < ../brk/rs1_cyc20.brk \ > rs1_H.disorder_out # # grep " H " rs1_H.disorder_out > rs1.H # # /bin/rm -rf d13w_H.disorder_out /bin/rm -rf rs1_H.disorder_out # # cat d13w.head d13w.H > d13wH.brk cat rs1.head rs1.H > rs1H.brk # # # o/p matrix will move XYZIN2 to XYZIN1 # # superpose XYZIN2 d13wH.brk\ XYZIN1 rs1H.brk\ MATRIX d13wH-to-rs1H.mat\ << 'EOF-superpose' 1 204 204 100 1 204 204 100 'EOF-superpose' # skewbrk XYZIN d13wH.brk\ XYZOUT d13wH-to-rs1H.brk\ MATRIX d13wH-to-rs1H.mat << eof eof # # brksort xyzin rs1H.brk xyzout rs1H_sort.brk brksort xyzin d13wH-to-rs1H.brk xyzout d13wH-to-rs1H_sort.brk # # # Clean up some more # /bin/rm -rf rs1H.brk /bin/rm -rf d13wH.brk /bin/rm -rf d13wH-to-rs1H.brk # #---- Run differences # #---- (i) for xyz # difres XYZIN1 rs1H_sort.brk \ XYZIN2 d13wH-to-rs1H_sort.brk\ PLOT rs1H-and-d13wH_xyz.plt\ << eof TITLE d13w/ rs1 H-chain XYZ !PLTY ! With this line commented out the picture is ! suitable for x84 - althouth the x84 picture is too ! big for the xterminals in the irc ! so use a scale function XSCALE 0.85 YSCALE 0.85 RESI H201 H316 eof # difres XYZIN1 rs1H_sort.brk \ XYZIN2 d13wH-to-rs1H_sort.brk\ PLOT rs1H-and-d13wH_temp.plt\ << eof TITLE d13w/ rs1 H-chain TEMP !PLTY ! With this line commented out the picture is ! suitable for x84 - althouth the x84 picture is too ! big for the xterminals in the irc ! so use a scale function XSCALE 0.85 YSCALE 0.85 RESI H201 H316 eof # # #---- Final Cleanup # /bin/rm -rf rs1H_sort.brk # # #---- Plot the files # pltdev -in rs1H-and-d13wH_temp.plt -out rs1H-and-d13wH_temp.ps -lan \ -xpos -3.0 -ypos3.0 -npict 1 -start 1 -lnwt 0.3 << eof y eof # cat $CCP/include/pl.header rs1H-and-d13wH_temp.ps\ > rs1H-and-d13wH_temp.ps.header mv rs1H-and-d13wH_temp.ps.header rs1H-and-d13wH_temp.ps # pltdev -in rs1H-and-d13wH_xyz.plt -out rs1H-and-d13wH_xyz.ps -lan \ -xpos -3.0 -ypos 3.0 -npict 1 -start 1 -lnwt 0.3 << eof y eof # # cat $CCP/include/pl.header rs1H-and-d13wH_xyz.ps\ > rs1H-and-d13wH_xyz.ps.header mv rs1H-and-d13wH_xyz.ps.header rs1H-and-d13wH_xyz.ps # pl rs1H-and-d13wH_xyz.ps pl rs1H-and-d13wH_temp.ps # # -- clean up /bin/rm -rf rs1H-and-d13wH_xyz.ps /bin/rm -rf rs1H-and-d13wH_xyz.plt /bin/rm -rf rs1H-and-d13wH_temp.ps /bin/rm -rf rs1H-and-d13wH_temp.plt # # # (ii) Remove disorder atoms # the awk script - removes B atoms in disorder # changes A to space in disorder # conformation # /bin/awk -f ${CETC}/disorder.awk < ../brk/d13w_cyc141.brk \ > d13w_L.disorder_out # # (iii) get L chain # grep " L " d13w_L.disorder_out > d13w.L # # /bin/awk -f ${CETC}/disorder.awk < ../brk/rs1_cyc20.brk \ > rs1_L.disorder_out # # grep " L " rs1_L.disorder_out > rs1.L # # /bin/rm -rf d13w_L.disorder_out /bin/rm -rf rs1_L.disorder_out # # cat d13w.head d13w.L > d13wL.brk cat rs1.head rs1.L > rs1L.brk # # # o/p matrix will move XYZIN2 to XYZIN1 # # superpose XYZIN2 d13wL.brk\ XYZIN1 rs1L.brk\ MATRIX d13wL-to-rs1L.mat\ << 'EOF-superpose' 1 3 3 100 1 3 3 100 'EOF-superpose' # skewbrk XYZIN d13wL.brk\ XYZOUT d13wL-to-rs1L.brk\ MATRIX d13wL-to-rs1L.mat << eof eof # # brksort xyzin rs1L.brk xyzout rs1L_sort.brk brksort xyzin d13wL-to-rs1L.brk xyzout d13wL-to-rs1L_sort.brk # # # Clean up some more # /bin/rm -rf rs1L.brk /bin/rm -rf d13wL.brk /bin/rm -rf d13wL-to-rs1L.brk # #---- Run differences # #---- (i) for xyz # difres XYZIN1 rs1L_sort.brk \ XYZIN2 d13wL-to-rs1L_sort.brk\ PLOT rs1L-and-d13wL_xyz.plt\ << eof TITLE d13w/ rs1 L-chain !PLTY ! With this line commented out the picture is ! suitable for x84 - althouth the x84 picture is too ! big for the xterminals in the irc ! so use a scale function XSCALE 0.85 YSCALE 0.85 XYZ RESI L1 L107 eof # difres XYZIN1 rs1L_sort.brk \ XYZIN2 d13wL-to-rs1L_sort.brk\ PLOT rs1L-and-d13wL_temp.plt\ << eof TITLE d13w/ rs1 L-chain !PLTY ! With this line commented out the picture is ! suitable for x84 - althouth the x84 picture is too ! big for the xterminals in the irc ! so use a scale function XSCALE 0.85 YSCALE 0.85 TEMP RESI L1 L107 eof # #---- Final Cleanup # /bin/rm -rf rs1L_sort.brk # # #---- Plot the files # pltdev -in rs1L-and-d13wL_temp.plt -out rs1L-and-d13wL_temp.ps -lan \ -xpos -3.0 -ypos 3.0 -npict 1 -start 1 -lnwt 0.3 << eof y eof # cat $CCP/include/pl.header rs1L-and-d13wL_temp.ps\ > rs1L-and-d13wL_temp.ps.header mv rs1L-and-d13wL_temp.ps.header rs1L-and-d13wL_temp.ps # pltdev -in rs1L-and-d13wL_xyz.plt -out rs1L-and-d13wL_xyz.ps -lan \ -xpos -3.0 -ypos 3.0 -npict 1 -start 1 -lnwt 0.3 << eof y eof # # cat $CCP/include/pl.header rs1L-and-d13wL_xyz.ps\ > rs1L-and-d13wL_xyz.ps.header mv rs1L-and-d13wL_xyz.ps.header rs1L-and-d13wL_xyz.ps # pl rs1L-and-d13wL_xyz.ps pl rs1L-and-d13wL_temp.ps # # -- clean up /bin/rm -rf rs1L-and-d13wL_xyz.ps /bin/rm -rf rs1L-and-d13wL_xyz.plt /bin/rm -rf rs1L-and-d13wL_temp.ps /bin/rm -rf rs1L-and-d13wL_temp.plt # # grep -v CRYSTL d13wH-to-rs1H_sort.brk > x.1 grep -v SCALE x.1 > d13wH-to-rs1H_sort.brk cat d13wL-to-rs1L_sort.brk d13wH-to-rs1H_sort.brk > d13w_mol.brk # # /bin/rm -rf d13w.head /bin/rm -rf d13wL-to-rs1L_sort.brk /bin/rm -rf d13wH-to-rs1H_sort.brk /bin/rm -rf x.1 /bin/rm -rf rs1.head # # /bin/rm -rf d13w.H /bin/rm -rf d13w.L /bin/rm -rf d13wH-to-rs1H.mat /bin/rm -rf d13wL-to-rs1L.mat /bin/rm -rf rs1.H /bin/rm -rf rs1.L /bin/rm -rf rs1H_sort.brk /bin/rm -rf rs1L_sort.brk # #---- Move d13w_mol.brk to frodo - add in rs1.rec #