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