Index of /ftp/pub/bmrb/timedomain/bmr19213/timedomain_data/dipo/hcaconJ/diff

[ICO]NameLast modifiedSizeDescription

[DIR]Parent Directory  -  
[   ]lowest_154.pse28-Jun-2014 02:53 835K 
[   ]xray.pse28-Jun-2014 02:53 699K 
[TXT]start.pdb28-Jun-2014 02:53 206K 
[TXT]lowest_187.pdb28-Jun-2014 02:53 206K 
[TXT]lowest_180.pdb28-Jun-2014 02:53 206K 
[TXT]lowest190.pdb28-Jun-2014 02:53 206K 
[TXT]lowest_162.pdb28-Jun-2014 02:53 206K 
[TXT]lowest_168.pdb28-Jun-2014 02:53 206K 
[TXT]lowest_167.pdb28-Jun-2014 02:53 206K 
[TXT]lowest_161.pdb28-Jun-2014 02:53 205K 
[TXT]lowest_164.pdb28-Jun-2014 02:53 205K 
[TXT]xray_h.pdb28-Jun-2014 02:53 181K 
[   ]D_NH_CAHA_all28-Jun-2014 02:53 20K 
[   ]D_NH_CAHA28-Jun-2014 02:53 20K 
[TXT]out.DC_NH_CAHA_xray_all28-Jun-2014 02:53 18K 
[TXT]out.DC_NH_CAHA_start_all28-Jun-2014 02:53 18K 
[   ]out.DC_NH_CAHA_xray28-Jun-2014 02:53 17K 
[   ]out.DC_NH_CAHA_start28-Jun-2014 02:53 17K 
[   ]comp_D_all.agr28-Jun-2014 02:53 12K 
[   ]D_NH_pf1_pb_xplor28-Jun-2014 02:53 11K 
[   ]comp_D.agr28-Jun-2014 02:53 11K 
[   ]comp_J.agr28-Jun-2014 02:53 9.8K 
[TXT]junk28-Jun-2014 02:53 9.3K 
[TXT]out.DC_CAHA_pf1_pb_avg_lowest_164_all28-Jun-2014 02:53 9.2K 
[TXT]out.DC_CAHA_pf1_pb_avg_xray_all28-Jun-2014 02:53 9.2K 
[   ]D_CAHA_pf1_pb_avg_flip28-Jun-2014 02:53 8.9K 
[   ]D_CAHA_pf1_pb_avg28-Jun-2014 02:53 8.9K 
[   ]D_CAHA_pf1_pb_avg_flip_all28-Jun-2014 02:53 8.9K 
[   ]D_CAHA_pf1_pb_avg_all28-Jun-2014 02:53 8.9K 
[TXT]out.DC_CAHA_pf1_pb_avg_lowest_180_all28-Jun-2014 02:53 8.8K 
[TXT]out.DC_CAHA_pf1_pb_avg_lowest_168_all28-Jun-2014 02:53 8.8K 
[TXT]out.DC_CAHA_pf1_pb_avg_lowest_167_all28-Jun-2014 02:53 8.8K 
[TXT]out.DC_CAHA_pf1_pb_avg_lowest_169_all28-Jun-2014 02:53 8.8K 
[TXT]out.DC_CAHA_pf1_pb_avg_start_all28-Jun-2014 02:53 8.7K 
[   ]D_CAHA_pf1_pb_avg_old28-Jun-2014 02:53 8.3K 
[   ]out.DC_CAHA_pf1_pb_avg_xray28-Jun-2014 02:53 7.7K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_16428-Jun-2014 02:53 7.7K 
[TXT]out.DC_CAHA_pf1_pb_lowest_164_all28-Jun-2014 02:53 7.6K 
[TXT]out.DC_CAHA_pf1_pb_3D_lowest_164_all28-Jun-2014 02:53 7.6K 
[TXT]out.DC_CAHA_pf1_pb_xray_all28-Jun-2014 02:53 7.6K 
[TXT]out.DC_CAHA_pf1_pb_start_all28-Jun-2014 02:53 7.6K 
[TXT]out.DC_CAHA_pf1_pb_3D_xray_all28-Jun-2014 02:53 7.6K 
[TXT]out.DC_CAHA_pf1_pb_3D_start_all28-Jun-2014 02:53 7.6K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_18028-Jun-2014 02:53 7.3K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_16928-Jun-2014 02:53 7.3K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_16828-Jun-2014 02:53 7.3K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_16728-Jun-2014 02:53 7.3K 
[   ]out.DC_CAHA_pf1_pb_avg_start28-Jun-2014 02:53 7.2K 
[   ]D_CAHA_pf1_pb_all28-Jun-2014 02:53 7.0K 
[   ]D_CAHA_pf1_pb_3D_all28-Jun-2014 02:53 7.0K 
[   ]D_CAHA_pf1_pb_3D28-Jun-2014 02:53 6.7K 
[   ]D_CAHA_pf1_pb28-Jun-2014 02:53 6.7K 
[   ]out.DC_CAHA_pf1_pb_xray28-Jun-2014 02:53 6.2K 
[   ]out.DC_CAHA_pf1_pb_start28-Jun-2014 02:53 6.2K 
[   ]out.DC_CAHA_pf1_pb_lowest_16428-Jun-2014 02:53 6.2K 
[   ]out.DC_CAHA_pf1_pb_3D_xray28-Jun-2014 02:53 6.2K 
[   ]out.DC_CAHA_pf1_pb_3D_start28-Jun-2014 02:53 6.2K 
[   ]out.DC_CAHA_pf1_pb_3D_lowest_16428-Jun-2014 02:52 6.2K 
[   ]J_CH_3D_vs_2D_pb_iso_all28-Jun-2014 02:53 4.9K 
[   ]J_CH_3D_vs_2D_pb_iso_all_old28-Jun-2014 02:53 4.9K 
[   ]out.DC_NH_CAHA_xray.dat28-Jun-2014 02:53 4.4K 
[   ]out.DC_NH_CAHA_start.dat28-Jun-2014 02:53 4.3K 
[   ]J_CH_3D_vs_2D_pb_pf1_all28-Jun-2014 02:53 3.4K 
[   ]J_CAHA_iso_pb_avg28-Jun-2014 02:53 3.3K 
[   ]J_CAHA_iso_pb_avg_old28-Jun-2014 02:53 3.3K 
[   ]diff_Jdip_flip.tcl28-Jun-2014 02:53 2.5K 
[   ]diff_Jdip.tcl28-Jun-2014 02:53 2.5K 
[   ]J_CAHA_iso_pb_3D28-Jun-2014 02:53 2.5K 
[   ]comp_J_all.tcl28-Jun-2014 02:53 2.3K 
[   ]J_CAHA_pf1_pb_avg_all28-Jun-2014 02:53 2.3K 
[   ]comp_J_avg.tcl28-Jun-2014 02:53 2.3K 
[   ]J_CAHA_pf1_pb_avg28-Jun-2014 02:53 2.3K 
[   ]J_CH_3D_vs_2D_pb_iso.dat28-Jun-2014 02:53 2.1K 
[   ]out.DC_CAHA_pf1_pb_avg_xray.dat28-Jun-2014 02:53 2.0K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_164.dat28-Jun-2014 02:53 2.0K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_180.dat28-Jun-2014 02:53 1.9K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_169.dat28-Jun-2014 02:53 1.9K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_168.dat28-Jun-2014 02:53 1.9K 
[   ]out.DC_CAHA_pf1_pb_avg_lowest_167.dat28-Jun-2014 02:53 1.9K 
[   ]out.DC_CAHA_pf1_pb_avg_start.dat28-Jun-2014 02:53 1.9K 
[   ]comp_J_dat.tcl28-Jun-2014 02:53 1.9K 
[   ]D_CAHA_pf1_pbn28-Jun-2014 02:53 1.8K 
[   ]out.DC_CAHA_pf1_pb_xray.dat28-Jun-2014 02:53 1.6K 
[   ]out.DC_CAHA_pf1_pb_start.dat28-Jun-2014 02:53 1.6K 
[   ]out.DC_CAHA_pf1_pb_3D_xray.dat28-Jun-2014 02:53 1.6K 
[   ]out.DC_CAHA_pf1_pb_3D_start.dat28-Jun-2014 02:53 1.6K 
[   ]out.DC_CAHA_pf1_pb_3D_lowest_164.dat28-Jun-2014 02:53 1.6K 
[   ]J_CH_3D_vs_2D_pb_iso.dat_old28-Jun-2014 02:53 1.6K 
[   ]D_CAHA_pf1_pb_avg_flip_col28-Jun-2014 02:53 1.6K 
[   ]D_CAHA_pf1_pb_avg_col28-Jun-2014 02:53 1.6K 
[   ]J_CAHA_pf1_pb_3D_all28-Jun-2014 02:53 1.5K 
[   ]J_CH_3D_vs_2D_pb_pf1.dat28-Jun-2014 02:53 1.5K 
[   ]J_CAHA_pf1_pb_3D28-Jun-2014 02:53 1.4K 
[   ]D_CAHA_pf1_pb_col28-Jun-2014 02:53 1.3K 
[   ]D_CAHA_pf1_pb_3D_col28-Jun-2014 02:53 1.3K 
[   ]J_CAHA_iso_pb_2D_all28-Jun-2014 02:53 1.1K 
[   ]J_CAHA_iso_pb_2D28-Jun-2014 02:53 1.0K 
[   ]J_CAHA_pf1_pb_2D_all28-Jun-2014 02:53 1.0K 
[   ]J_CAHA_pf1_pb_2D28-Jun-2014 02:53 926  
[   ]J_CAHA_iso_pb_2D_all_old28-Jun-2014 02:53 926  
[   ]J_CAHA_iso_pb_2D_old28-Jun-2014 02:53 887  

***

DC program: For Gly use HA# and the measured Gly sum of CAHA2+CAHA3 couplings as is (don't divide by 2)!!! GLYs are not used for getting the alignment tensor by SVD, their RDC values are just back-calculated from the structure (once the alignment tensor is obtained by SVD of the other RDCs).

xplor-nih: For Gly use HA# and the measured Gly sum of CAHA2+CAHA3 couplings as is (don't divide by 2)!!! and make a separate file with those (DCAHA_bicelle_gly.tbl), maybe scale them to NH, then use in xplor input script:

   class glyb
    type fixd
    sign on
    average sum
    force $kdipo_CH
    potential harmonic
    coef 0.0 $da $rhom
    @DCAHA_bicelle_gly.tbl	 				{* uses axis 500 *}



******************************************************************************
*** using 3D pf1 and 3D iso is worst.

diff_Jdip.tcl > D_CAHA_pf1_pb_3D_col
convert_pales_DC_CAHA.tcl D_CAHA_pf1_pb_3D_col lowest_164.pdb > D_CAHA_pf1_pb_3D_all
cp D_CAHA_pf1_pb_3D_all D_CAHA_pf1_pb_3D
took out resID 2

DC -inD D_CAHA_pf1_pb_3D -pdb xray_h.pdb -verb > out.DC_CAHA_pf1_pb_3D_xray_all
DC -inD D_CAHA_pf1_pb_3D -pdb xray_h.pdb -verb > out.DC_CAHA_pf1_pb_3D_xray
n out.DC_CAHA_pf1_pb_3D_xray&
getCols out.DC_CAHA_pf1_pb_3D_xray out.DC_CAHA_pf1_pb_3D_xray.dat 7 8 0

xmgr comp_D.agr &

rmsd.tcl out.DC_CAHA_pf1_pb_3D_xray.dat
n= 77 rmsd= 8.3
difference > 1.5*rmsd:
   38   14.9
    4  -15.2
   32   15.7
  150   15.7
   47  -15.8
  113  -15.9
   97  -16.0
  164   27.8
   35   31.5

took out: 35, 164
n= 75 rmsd= 6.7
difference > 1.5*rmsd:
   68  -10.2
   16  -10.7
  117  -11.5
   38   13.5
  113  -14.3
   32   15.0
   47  -15.3
    4  -15.4
  150   15.9
   97  -16.9

DC -inD D_CAHA_pf1_pb_3D -pdb lowest_164.pdb -verb > out.DC_CAHA_pf1_pb_3D_lowest_164_all
DC -inD D_CAHA_pf1_pb_3D -pdb lowest_164.pdb -verb > out.DC_CAHA_pf1_pb_3D_lowest_164
n out.DC_CAHA_pf1_pb_3D_lowest_164&
getCols out.DC_CAHA_pf1_pb_3D_lowest_164 out.DC_CAHA_pf1_pb_3D_lowest_164.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_3D_lowest_164.dat
n= 75 rmsd=12.0
difference > 1.5*rmsd:
   38   20.1
   77   20.1
  159   20.7
   68   22.9
   97  -24.7
  105   34.4
   69  -48.1

rmsd.tcl out.DC_CAHA_pf1_pb_3D_start.dat
n= 75 rmsd=12.0
difference > 1.5*rmsd:
   32   18.4
   38   18.7
   97  -20.5
   73   20.6
   68   21.4
  105   24.2
   89  -34.1
   69  -48.4


******************************************************************************
*** using 3D pf1 and avg iso is a bit better:

comp_J_all.tcl > J_CH_3D_vs_2D_pb_iso_all
comp_J_dat.tcl > J_CH_3D_vs_2D_pb_iso.dat

xmgr comp_J.agr

comp_J_avg.tcl > J_CAHA_iso_pb_avg

diff_Jdip.tcl > D_CAHA_pf1_pb_col
convert_pales_DC_CAHA.tcl D_CAHA_pf1_pb_col lowest_164.pdb > D_CAHA_pf1_pb_all
cp D_CAHA_pf1_pb_all D_CAHA_pf1_pb
n  D_CAHA_pf1_pb&
took out resID 2

DC -inD D_CAHA_pf1_pb -pdb xray_h.pdb -verb > out.DC_CAHA_pf1_pb_xray_all
DC -inD D_CAHA_pf1_pb -pdb xray_h.pdb -verb > out.DC_CAHA_pf1_pb_xray
n out.DC_CAHA_pf1_pb_xray &
getCols out.DC_CAHA_pf1_pb_xray out.DC_CAHA_pf1_pb_xray.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_xray.dat

n= 77 rmsd= 8.0
difference > 1.5*rmsd:
   47  -12.2
   32   13.0
   38   14.9
    4  -15.1
   97  -15.5
  150   15.9
  113  -16.4
  164   27.5
   35   31.4

took out: 35, 164

n= 75 rmsd= 6.4
difference > 1.5*rmsd:
    3    9.6
  117   -9.8
   68  -10.1
   47  -11.7
   32   12.3
   38   13.5
  113  -14.7
    4  -15.2
  150   16.0
   97  -16.4

xmgr comp_D.agr &

DC -inD D_CAHA_pf1_pb -pdb lowest_164.pdb -verb > out.DC_CAHA_pf1_pb_lowest_164_all
DC -inD D_CAHA_pf1_pb -pdb lowest_164.pdb -verb > out.DC_CAHA_pf1_pb_lowest_164
n out.DC_CAHA_pf1_pb_3D_lowest_164&
getCols out.DC_CAHA_pf1_pb_3D_lowest_164 out.DC_CAHA_pf1_pb_3D_lowest_164.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_3D_lowest_164.dat
n= 75 rmsd=12.0
difference > 1.5*rmsd:
   38   20.1
   77   20.1
  159   20.7
   68   22.9
   97  -24.7
  105   34.4
   69  -48.1

rmsd.tcl out.DC_CAHA_pf1_pb_start.dat
n= 75 rmsd=11.7
difference > 1.5*rmsd:
   77   17.7
   38   18.6
   97  -20.1
   73   21.0
   68   21.1
  105   25.6
   89  -34.0
   69  -47.9


******************************************************************************
*** using avg pf1 and iso:

comp_J_all.tcl > J_CH_3D_vs_2D_pb_pf1_all
comp_J_dat.tcl > J_CH_3D_vs_2D_pb_pf1.dat

xmgr comp_J.agr

comp_J_avg.tcl > J_CAHA_pf1_pb_avg

took out from 2D:
17, 30, 52, 140
kept C29, A106, better than 3D

*** took out from 3D:
29, 106

diff_Jdip.tcl > D_CAHA_pf1_pb_avg_col
convert_pales_DC_CAHA.tcl D_CAHA_pf1_pb_avg_col lowest_164.pdb > D_CAHA_pf1_pb_avg_all
cp D_CAHA_pf1_pb_avg_all D_CAHA_pf1_pb_avg
n  D_CAHA_pf1_pb_avg&
took out resID 2

DC -inD D_CAHA_pf1_pb_avg -pdb xray_h.pdb -verb > out.DC_CAHA_pf1_pb_avg_xray_all
DC -inD D_CAHA_pf1_pb_avg -pdb xray_h.pdb -verb > out.DC_CAHA_pf1_pb_avg_xray
n out.DC_CAHA_pf1_pb_avg_xray &
getCols out.DC_CAHA_pf1_pb_avg_xray out.DC_CAHA_pf1_pb_avg_xray.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_avg_xray.dat
n= 99 rmsd= 7.9
difference > 1.5*rmsd:
   32   12.0
  113  -12.5
   42  -13.8
  150   13.9
   38   15.0
   97  -15.0
    4  -15.2
  120   17.3
   80  -18.6
    7  -21.7
  164   26.6
   35   32.2

took out: 35, 164, 7
n= 96 rmsd= 6.3
difference > 1.5*rmsd:
   39    9.9
  159  -10.0
  113  -11.2
   32   11.8
   38   13.7
  150   14.2
   42  -14.8
    4  -16.1
   97  -16.1
   80  -17.4
  120   17.6

took out 2 minors:
n= 94 rmsd= 6.3
difference > 1.5*rmsd:
   39   10.0
  159  -10.0
  113  -11.3
   32   11.8
   38   13.9
  150   13.9
   42  -14.5
    4  -16.0
   97  -16.1
   80  -17.3
  120   17.5


DC -inD D_CAHA_pf1_pb_avg -pdb lowest_164.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_164_all
DC -inD D_CAHA_pf1_pb_avg -pdb lowest_164.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_164
n out.DC_CAHA_pf1_pb_avg_lowest_164 &
getCols out.DC_CAHA_pf1_pb_avg_lowest_164 out.DC_CAHA_pf1_pb_avg_lowest_164.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_avg_lowest_164.dat
n= 94 rmsd=11.3
difference > 1.5*rmsd:
  120   17.2
   22  -17.6
   87  -19.0
   73   19.0
   77   19.6
   80  -19.9
   38   20.5
   42  -20.7
  159   21.6
   68   23.2
   57   23.3
   97  -24.7
  105   31.1
   69  -46.8

rmsd.tcl out.DC_CAHA_pf1_pb_avg_start.dat
n= 94 rmsd=11.8
difference > 1.5*rmsd:
    8   17.8
  120   18.3
   80  -19.1
   97  -20.5
  105   20.8
   38   21.4
   73   21.6
   42  -21.7
   57   23.4
   68   23.9
   93  -25.0
   89  -30.1
   69  -45.5

*** 
cp D_CAHA_pf1_pb_avg /home/noi/work/xplor/pixj/work

*** run 167 used CAHA RDCs:

DC -inD D_CAHA_pf1_pb_avg -pdb lowest_167.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_167_all
DC -inD D_CAHA_pf1_pb_avg -pdb lowest_167.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_167
n out.DC_CAHA_pf1_pb_avg_lowest_167 &
getCols out.DC_CAHA_pf1_pb_avg_lowest_167 out.DC_CAHA_pf1_pb_avg_lowest_167.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_avg_lowest_167.dat
n= 95 rmsd= 5.8
difference > 1.5*rmsd:
   47   -8.9
  141    8.9
   39    9.0
   87   -9.1
  117   -9.1
   73    9.3
   19   -9.5
   83   10.4
   34  -10.7
  106   11.7
  134  -12.4
   80  -13.7
   69  -14.6
   57   16.1

took out: 57, 69, 80, 134, 34
used major for: 88
used only 3D for:106

n= 89 rmsd= 4.8
difference > 1.5*rmsd:
   40    8.1
  105    8.3
   38    8.5
   39    8.8
  141    8.8
  117   -8.9
   73    8.9
   87   -8.9
   47   -9.1
   19   -9.5
   83    9.7

*** run 168 same weight DNH/DCAHA

DC -inD D_CAHA_pf1_pb_avg -pdb lowest_168.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_168_all
DC -inD D_CAHA_pf1_pb_avg -pdb lowest_168.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_168
n out.DC_CAHA_pf1_pb_avg_lowest_168 &
getCols out.DC_CAHA_pf1_pb_avg_lowest_168 out.DC_CAHA_pf1_pb_avg_lowest_168.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_avg_lowest_168.dat

n= 89 rmsd= 5.1
difference > 1.5*rmsd:
   47   -7.9
   19   -8.0
   97   -8.2
   42   -8.5
  117   -8.7
   30   -8.7
   73    8.8
   91    8.9
   38    8.9
   89   -9.5
  141   10.0
   40   11.0
  105   11.1
   68   14.0

*** run 169
adjusted weight of CAHA according to exp. errors

DC -inD D_CAHA_pf1_pb_avg -pdb start.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_169_all
DC -inD D_CAHA_pf1_pb_avg -pdb start.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_169
n out.DC_CAHA_pf1_pb_avg_lowest_169 &
getCols out.DC_CAHA_pf1_pb_avg_lowest_169 out.DC_CAHA_pf1_pb_avg_lowest_169.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_avg_lowest_169.dat


*** run 180
DC -inD D_CAHA_pf1_pb_avg -pdb lowest_180.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_180_all
DC -inD D_CAHA_pf1_pb_avg -pdb lowest_180.pdb -verb > out.DC_CAHA_pf1_pb_avg_lowest_180
n out.DC_CAHA_pf1_pb_avg_lowest_180 &
getCols out.DC_CAHA_pf1_pb_avg_lowest_180 out.DC_CAHA_pf1_pb_avg_lowest_180.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_avg_lowest_180.dat
n= 89 rmsd= 6.3
difference > 1.5*rmsd:
   38    9.8
   40   11.1
  120   11.2
   42  -11.2
   87  -11.9
   73   13.7
  105   14.8
   89  -17.2
   68   18.9

xmgr comp_D.agr

*** run 182
adjusted weight of CAHA according to exp. errors

DC -inD D_CAHA_pf1_pb_avg -pdb start.pdb -verb > out.DC_CAHA_pf1_pb_avg_start_all
DC -inD D_CAHA_pf1_pb_avg -pdb start.pdb -verb > out.DC_CAHA_pf1_pb_avg_start
n out.DC_CAHA_pf1_pb_avg_start &
getCols out.DC_CAHA_pf1_pb_avg_start out.DC_CAHA_pf1_pb_avg_start.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_avg_start.dat
n= 89 rmsd= 6.2
difference > 1.5*rmsd:
   19   -9.4
   97   -9.5
   42   -9.5
   38    9.6
  141    9.8
   93  -10.0
  120   10.3
   77   10.8
   87  -10.9
  105   12.6
   73   13.0
   89  -15.6
   68   19.3

xmgr comp_D.agr

*** run 183
DC -inD D_CAHA_pf1_pb_avg -pdb start.pdb -verb > out.DC_CAHA_pf1_pb_avg_start_all
DC -inD D_CAHA_pf1_pb_avg -pdb start.pdb -verb > out.DC_CAHA_pf1_pb_avg_start
n out.DC_CAHA_pf1_pb_avg_start &
getCols out.DC_CAHA_pf1_pb_avg_start out.DC_CAHA_pf1_pb_avg_start.dat 7 8 0
rmsd.tcl out.DC_CAHA_pf1_pb_avg_start.dat
n= 89 rmsd= 6.4
difference > 1.5*rmsd:
   30   -9.9
   38   10.3
   42  -10.9
  120   11.4
   73   11.4
   97  -12.2
   87  -12.2
   89  -12.7
  105   13.1
   40   14.1
   68   23.0

xmgr comp_D.agr

*** run 189

n= 89 rmsd= 5.6
difference > 1.5*rmsd:
  141    8.4
   47   -8.7
  140   -8.8
  150    8.8
   87   -9.0
  105    9.4
   38    9.5
   19   -9.7
   97   -9.7
   73    9.8
   83   10.0
  117  -11.7
  120   11.7
   42  -12.0
   68   18.2

take out 68:
n= 88 rmsd= 5.2
difference > 1.5*rmsd:
  141    8.0
  140   -8.1
  150    8.2
   87   -8.7
   19   -8.7
   47   -8.9
   73    9.4
  105    9.5
   38    9.6
   83    9.9
   97  -10.3
  117  -11.7
   42  -12.5
  120   12.6

*** join / combine CAHA with NH, needed a sign flip:

diff_Jdip_flip.tcl > D_CAHA_pf1_pb_avg_flip_col
convert_pales_DC_CAHA.tcl D_CAHA_pf1_pb_avg_flip_col lowest_164.pdb > D_CAHA_pf1_pb_avg_flip_all
cp D_CAHA_pf1_pb_avg_flip_all D_CAHA_pf1_pb_avg_flip
some manual edits:
tkdiff D_CAHA_pf1_pb_avg_flip D_CAHA_pf1_pb_avg

cat D_NH_pf1_pb_xplor D_CAHA_pf1_pb_avg_flip > D_NH_CAHA_all
cp D_NH_CAHA_all D_NH_CAHA

DC -inD D_NH_CAHA -pdb start.pdb -verb > out.DC_NH_CAHA_start_all
DC -inD D_NH_CAHA -pdb start.pdb -verb > out.DC_NH_CAHA_start

n out.DC_NH_CAHA_start &
getCols out.DC_NH_CAHA_start out.DC_NH_CAHA_start.dat 7 8 0
rmsd.tcl out.DC_NH_CAHA_start.dat

xmgr comp_D.agr

DC -inD D_NH_CAHA -pdb xray_h.pdb -verb > out.DC_NH_CAHA_xray_all
DC -inD D_NH_CAHA -pdb xray_h.pdb -verb > out.DC_NH_CAHA_xray

getCols out.DC_NH_CAHA_xray out.DC_NH_CAHA_xray.dat 7 8 0
rmsd.tcl out.DC_NH_CAHA_xray.dat

- to get an accurate alignment, took out 38, 120, 140

DC -inD D_NH_CAHA -pdb start.pdb -verb > out.DC_NH_CAHA_start_all
DC -inD D_NH_CAHA -pdb start.pdb -verb > out.DC_NH_CAHA_start

n out.DC_NH_CAHA_start &
getCols out.DC_NH_CAHA_start out.DC_NH_CAHA_start.dat 7 8 0

Da=8.75/Dr=0.44












*** imposed NH fitted align. tensor:
DC -saupe 1.0422e-04  8.8844e-04 -7.4057e-04 -6.7992e-05 -2.3899e-049.3213e-05 8.7169e-04 -7.3993e-04 -7.8232e-05 -2.4600e-04 -inD D_CAHA_bicelle_w_o_outliers -pdb lowest _113.pdb -verb

*** imposed NH and CH fitted align. tensor:

DC -saupe 1.0422e-04 8.8844e-04 -7.4057e-04 -6.7992e-05 -2.3899e-04 -inD D_CAHA_bicelle_w_o_outliers -pdb lowest_113.pdb -verb

- removed GLYs, NTD:17, 26, 27, A37 (ovl.), V64 (peaks shiftd in pf1 at pH 8.0, iso @ pH 8.5), S112 (too weak, mobile loop), H139 (too weak), :

*** compare bicelle_sds with pf1:

join_cols.tcl > out.join_pf1_bicelle_sds_compare.dat

xmgr comp_D.agr

correlation factor is 95% !

getCols out.DC_CAHA_bicelle_377 out.DC_CAHA_bicelle_377.dat 7 8 0
 rmsd.tcl out.DC_CAHA_bicelle_377.dat
n=110 rmsd= 3.6
difference > 2.0*rmsd:
  130    7.3
  105    7.6
  169   -7.9
   79    9.2
  100   -9.7
   98  -10.3
  109  -12.7