Index of /ftp/pub/bmrb/timedomain/bmr19213/timedomain_data/dipo/ipapfhsqc/diff
- averaged if diff smaller than 1 Hz:
comp_J.tcl > J_NH_iso_3D_vs_2D_pb
cp J_NH_iso_3D_vs_2D_pb J_NH_iso_pb
- averaged if diff smaller than 1Hz; kept values closer to -94 Hz; preferred the better 3D spectrum:
J_NH_iso_pb
comp_J.tcl > J_NH_3D_vs_2D_pb_pf1
diff_Jdip.tcl > D_NH_pf1_pb_col
diff_Jdip.tcl > D_NH_pf1_pb_coln
diff_Jdip.tcl > D_NH_pf1_pb_colnn
convert_pales_DC_NH.tcl D_NH_pf1_pb_coln lowest_111.pdb > D_NH_pf1_pb_all
convert_pales_DC_NH.tcl D_NH_pf1_pb_coln lowest_111.pdb > D_NH_pf1_pb
DC -inD D_NH_pf1_pb -pdb lowest_111.pdb -verb > junk
getCols junk junk.dat 7 8 0
rmsd.tcl junk.dat
DC -inD D_NH_pf1_pb_all -pdb lowest_129.pdb -verb > junk
- used all as constraints in run 154:
DC -inD D_NH_pf1_pb -pdb lowest_154.pdb -verb > out.DC_info
DC -inD D_NH_pf1_pb -pdb lowest_154.pdb -verb > out.DC
n out.DC&
getCols out.DC out.DC.dat 7 8 0
rmsd.tcl out.DC.dat
*** use best RDCs for a more accurate align. tensor:
DC -inD D_NH_pf1_pb_align -pdb lowest_154.pdb -verb > out.DC_info
DC -inD D_NH_pf1_pb_align -pdb lowest_154.pdb -verb > out.DC
n out.DC&
getCols out.DC out.DC.dat 7 8 0
rmsd.tcl out.DC.dat
- also took out minor RDCs that were in less agreement with this alignment:
tkdiff D_NH_pf1_pb D_NH_pf1_pb_all
*** NOTE !!! ****
- 2 conformers: V42, D59, V61, V72, R76, Q81, Q98, L99, V104, N107, V109, L121, H125, Q126, W133 - mostly around ring D, and supporting the model of signaling to the 2 long helices at the termini (dimer interface)!
also E73, R100, I138 - v. small minor (from hnco_nh)
- RDCs of the minor conformers seem to fit better lowest_154.pdb (best fit as of 10/26/2011)
*** outliers:
- large: R58, E69
- medium: E63, H95, I136, D139
*** 3D on 3 mm Shigemi (little) sample from Joe, pf1, in pb
J_NH_pf1_pb_3D - for conformers picked the value close to ipap
*****************************************************************************************
chosen pf1 RDCs that best fit lowest_151.pdb
DC -inD D_NH_pf1_pb -pdb lowest_154.pdb -verb > out.DC_154
cp out.DC_154 out.DC_154_info
getCols out.DC_154 out.DC_154.dat 7 8 0
rmsd.tcl out.DC.dat
n=132 rmsd= 1.8
difference > 1.5*rmsd:
150 2.7
64 -3.1
63 -3.1
116 -3.1
73 3.2
30 -3.4
88 -3.7
53 4.2
67 5.1
95 -5.2
58 7.8
69 -7.9
*** outliers:
- large: R58, E69 - excluded
DC -inD D_NH_pf1_pb -pdb lowest_154.pdb -verb > out.DC_154
cp out.DC_154 out.DC_154_info
getCols out.DC_154 out.DC_154.dat 7 8 0
rmsd.tcl out.DC.dat
n=107 rmsd= 1.3
difference > 1.5*rmsd:
34 1.9
119 -2.1
143 2.4
29 2.4
54 -2.4
79 -2.5
85 2.5
63 -2.6
48 -2.6
41 2.7
73 2.7
150 2.8
64 -3.0
*** keep only the best fitting conformer for xplor:
cp D_NH_pf1_pb D_NH_pf1_pb_xplor
*** xray
not so good:
xplor -py buildpsf.py > out.buildpsf
better: molmol:
molmol2xplor.tcl xray_h_molmol.pdb > xray_h.pdb
replace ARG+ with ARG etc.
DC -inD D_NH_pf1_pb_all -pdb xray_h.pdb -verb > out.DC_xray_all
DC -inD D_NH_pf1_pb_all -pdb xray_h.pdb -verb > out.DC_xray
getCols out.DC_xray out.DC_xray.dat 7 8 0
rmsd.tcl out.DC_xray.dat
n=134 rmsd= 3.2
difference > 1.5*rmsd:
52 4.8
84 5.2
58 5.5
150 5.6
22 6.1
5 -6.5
155 6.8
73 7.7
44 10.9
18 -13.6
4 14.3
DC -inD D_NH_pf1_pb_xray -pdb xray_h.pdb -verb > out.DC_xray_info
DC -inD D_NH_pf1_pb_xray -pdb xray_h.pdb -verb > out.DC_xray
getCols out.DC_xray out.DC_xray.dat 7 8 0
rmsd.tcl out.DC_xray.dat
n=131 rmsd= 2.5
difference > 1.5*rmsd:
39 3.8
66 3.8
131 4.2
60 4.2
139 -4.3
58 4.5
115 -4.5
96 4.7
150 4.8
42 -4.9
42 -4.9
84 5.1
52 5.2
22 5.3
5 -5.6
155 6.4
73 8.6
...
n=114 rmsd= 2.2
difference > 1.5*rmsd:
136 -3.4
49 -3.5
69 -3.6
31 -3.6
39 3.9
58 4.0
60 4.1
131 4.1
42 -4.3
115 -4.4
150 4.5
139 -4.6
84 4.9
22 5.0
5 -5.1
96 5.3
52 5.4
*** lowest_163.pdb
DC -inD D_NH_pf1_pb_xplor -pdb lowest_163.pdb -verb > out.DC_163_all
DC -inD D_NH_pf1_pb_xplor -pdb lowest_163.pdb -verb > out.DC_163
getCols out.DC_163 out.DC_163.dat 7 8 0
rmsd.tcl out.DC_163.dat
n=118 rmsd= 1.9
difference > 1.5*rmsd:
76 3.0
107 -3.2
84 3.3
96 3.5
118 3.6
87 4.2
69 4.2
71 -4.6
63 -5.2
95 -5.2
58 9.7
*** flipped the sign of NH RDCs in /home/noi/work/xplor/pixj/work (XPLOR convention)
DC -inD D_NH_pf1_pb_xplor -pdb start.pdb -verb > out.DC_start_all
DC -inD D_NH_pf1_pb_xplor -pdb start.pdb -verb > out.DC_start
getCols out.DC_start out.DC_start.dat 7 8 0
rmsd.tcl out.DC_start.dat
n=118 rmsd= 1.7
difference > 1.5*rmsd:
84 2.8
39 2.8
87 2.9
108 -2.9
69 3.2
99 -3.3
63 -3.4
107 -3.7
95 -6.0
58 10.0
*** for Da/R only:
DC -inD D_NH_pf1_pb_xplor_test -pdb start.pdb -verb > junk_all
getCols junk junk.dat 7 8 0
rmsd.tcl junk.dat
*** run 189
DC -inD D_NH_pf1_pb_xplor -pdb start.pdb -verb > out.DC_start_all
DC -inD D_NH_pf1_pb_xplor -pdb start.pdb -verb > out.DC_start
n out.DC_start &
getCols out.DC_start out.DC_start.dat 7 8 0
rmsd.tcl out.DC_start.dat
n=118 rmsd= 1.6
difference > 1.5*rmsd:
36 -2.4
150 2.4
76 2.5
84 2.5
108 -2.6
138 2.6
107 -2.8
69 2.9
60 3.0
116 -3.2
87 4.1
95 -5.9
58 7.6
*** added a few more iso RDCs from artsy:
diff_Jdip.tcl > D_NH_pf1_pb_colnnn
convert_pales_DC_NH.tcl D_NH_pf1_pb_colnnn lowest_199.pdb > D_NH_pf1_pb_allnn
DC -inD D_NH_pf1_pb_xplor -pdb lowest_199.pdb -verb > out.DC_199_all
DC -inD D_NH_pf1_pb_xplor -pdb lowest_199.pdb -verb > out.DC_199
n out.DC_199
getCols out.DC_199 out.DC_199.dat 7 8 0
rmsd.tcl out.DC_199.dat
n=118 rmsd= 1.4
difference > 1.5*rmsd:
67 -2.3
139 -2.3
150 2.6
108 -2.6
36 -2.7
84 2.9
116 -3.0
71 -3.6
96 3.6
95 -4.3
73 4.8
107 -5.0
diff_Jdip.tcl > D_NH_pf1_pb_col
- added manually RDCs from artsy in:
D_NH_pf1_pb_col
convert_pales_DC_NH.tcl D_NH_pf1_pb_col lowest_199.pdb > D_NH_pf1_pb_allnnn
cp D_NH_pf1_pb_allnnn D_NH_pf1_pb_xplorn
DC -inD D_NH_pf1_pb_xplorn -pdb lowest_199.pdb -verb > out.DC_199_all
DC -inD D_NH_pf1_pb_xplorn -pdb lowest_199.pdb -verb > out.DC_199
n out.DC_199
getCols out.DC_199 out.DC_199.dat 7 8 0
rmsd.tcl out.DC_199.dat
n=142 rmsd= 1.9
difference > 1.5*rmsd:
59 3.1
59 3.1
98 3.3
98 3.3
19 -3.3
72 -3.6
72 -3.6
103 -3.8
164 4.0
96 4.0
71 -4.1
95 -4.2
90 -4.4
73 5.2
105 -5.6
70 -6.8
9 7.2
*** pg Pg ***
J_NH_pf1_pg_2D from ipap, iso pg as artsy!
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