Index of /ftp/pub/bmrb/entry_directories/bmr19214/timedomain_data/dipo/ipapfhsqc/diff

[ICO]NameLast modifiedSizeDescription
[PARENTDIR]Parent Directory   -  
[ ]DNH_pf1_pb.tbl 2021-02-13 20:17 26K 
[ ]D_NH_pb_artsy_unique..>2021-02-13 20:18 176  
[ ]D_NH_pf1_pb 2021-02-13 20:16 11K 
[ ]D_NH_pf1_pb_129 2021-02-13 20:17 12K 
[ ]D_NH_pf1_pb_align 2021-02-13 20:16 9.4K 
[ ]D_NH_pf1_pb_all 2021-02-13 20:16 12K 
[ ]D_NH_pf1_pb_alln 2021-02-13 20:17 12K 
[ ]D_NH_pf1_pb_allnn 2021-02-13 20:16 12K 
[ ]D_NH_pf1_pb_allnnn 2021-02-13 20:17 13K 
[ ]D_NH_pf1_pb_artsy_un..>2021-02-13 20:16 946  
[ ]D_NH_pf1_pb_col 2021-02-13 20:17 2.4K 
[ ]D_NH_pf1_pb_col_ass 2021-02-13 20:16 2.4K 
[ ]D_NH_pf1_pb_coln 2021-02-13 20:16 2.1K 
[ ]D_NH_pf1_pb_coln_ass 2021-02-13 20:17 2.4K 
[ ]D_NH_pf1_pb_colnn 2021-02-13 20:18 2.1K 
[ ]D_NH_pf1_pb_colnn_ass 2021-02-13 20:17 2.4K 
[ ]D_NH_pf1_pb_colnn_assn 2021-02-13 20:17 2.4K 
[ ]D_NH_pf1_pb_colnnn 2021-02-13 20:17 2.1K 
[ ]D_NH_pf1_pb_w_trp 2021-02-13 20:18 12K 
[ ]D_NH_pf1_pb_xplor 2021-02-13 20:16 11K 
[ ]D_NH_pf1_pb_xplor_old 2021-02-13 20:18 11K 
[ ]D_NH_pf1_pb_xplor_test 2021-02-13 20:17 11K 
[ ]D_NH_pf1_pb_xplorn 2021-02-13 20:16 13K 
[ ]D_NH_pf1_pb_xray 2021-02-13 20:18 12K 
[ ]J_NH_3D_vs_2D_pb_pf1 2021-02-13 20:16 4.6K 
[ ]J_NH_pf1_pb 2021-02-13 20:17 2.4K 
[ ]J_NH_pf1_pb_3D 2021-02-13 20:18 1.9K 
[ ]J_NH_pf1_pb_3D_orig 2021-02-13 20:16 2.3K 
[ ]J_NH_pf1_pb_all 2021-02-13 20:16 2.4K 
[ ]J_NH_pf1_pb_orig 2021-02-13 20:17 2.4K 
[ ]J_NH_pf1_pg_2D 2021-02-13 20:18 1.6K 
[ ]J_iso_pb 2021-02-13 20:17 2.5K 
[ ]J_iso_pb_2D 2021-02-13 20:17 2.7K 
[ ]J_iso_pb_3D 2021-02-13 20:16 2.9K 
[ ]J_iso_pb_3D_vs_2D 2021-02-13 20:17 5.5K 
[ ]J_iso_pb_3D_vs_2D_all 2021-02-13 20:16 5.5K 
[ ]J_iso_pb_3D_vs_2D_al..>2021-02-13 20:18 3.6K 
[ ]anis_NH_tbl.awk 2021-02-13 20:16 679  
[ ]avg_J.tcl 2021-02-13 20:18 2.3K 
[TXT]buildpsf.inp 2021-02-13 20:16 507  
[TXT]buildpsf.py 2021-02-13 20:16 1.3K 
[ ]comp_D.agr 2021-02-13 20:17 11K 
[ ]comp_J.agr 2021-02-13 20:18 11K 
[ ]comp_J.tcl 2021-02-13 20:16 2.4K 
[ ]convert_pales_DC_NH.tcl2021-02-13 20:16 1.2K 
[ ]cyc_impr_bridge_flex..>2021-02-13 20:17 45K 
[ ]cyc_impr_bridge_flex..>2021-02-13 20:17 34K 
[ ]diff_Jdip.tcl 2021-02-13 20:18 2.4K 
[TXT]junk 2021-02-13 20:17 16K 
[TXT]junk.dat 2021-02-13 20:17 7.4K 
[TXT]junk_all 2021-02-13 20:17 11K 
[TXT]lowest_111.pdb 2021-02-13 20:17 205K 
[TXT]lowest_129.pdb 2021-02-13 20:16 205K 
[TXT]lowest_143.pdb 2021-02-13 20:16 205K 
[TXT]lowest_144.pdb 2021-02-13 20:17 205K 
[TXT]lowest_150.pdb 2021-02-13 20:17 205K 
[TXT]lowest_153.pdb 2021-02-13 20:16 205K 
[TXT]lowest_154.pdb 2021-02-13 20:16 206K 
[ ]lowest_154.pse 2021-02-13 20:17 835K 
[TXT]lowest_155.pdb 2021-02-13 20:17 206K 
[TXT]lowest_156.pdb 2021-02-13 20:16 206K 
[TXT]lowest_157.pdb 2021-02-13 20:17 206K 
[TXT]lowest_160.pdb 2021-02-13 20:16 205K 
[TXT]lowest_161.pdb 2021-02-13 20:17 205K 
[TXT]lowest_162.pdb 2021-02-13 20:16 206K 
[TXT]lowest_163.pdb 2021-02-13 20:16 206K 
[TXT]lowest_167.pdb 2021-02-13 20:16 206K 
[TXT]lowest_168.pdb 2021-02-13 20:17 206K 
[TXT]lowest_199.pdb 2021-02-13 20:16 206K 
[TXT]model_orig.pdb 2021-02-13 20:17 80K 
[ ]molmol2xplor.tcl 2021-02-13 20:17 3.6K 
[TXT]new.pdb 2021-02-13 20:17 184K 
[ ]out.DC 2021-02-13 20:17 8.8K 
[ ]out.DC.dat 2021-02-13 20:16 2.3K 
[ ]out.DC_154 2021-02-13 20:16 11K 
[ ]out.DC_154.dat 2021-02-13 20:17 2.8K 
[TXT]out.DC_154_all 2021-02-13 20:16 13K 
[TXT]out.DC_154_info 2021-02-13 20:17 12K 
[TXT]out.DC_155_all 2021-02-13 20:18 12K 
[TXT]out.DC_156_all 2021-02-13 20:16 12K 
[ ]out.DC_163 2021-02-13 20:17 9.7K 
[ ]out.DC_163.dat 2021-02-13 20:17 2.5K 
[TXT]out.DC_163_all 2021-02-13 20:16 11K 
[ ]out.DC_199 2021-02-13 20:18 12K 
[ ]out.DC_199.dat 2021-02-13 20:17 3.1K 
[TXT]out.DC_199_all 2021-02-13 20:16 16K 
[TXT]out.DC_all 2021-02-13 20:18 11K 
[TXT]out.DC_info 2021-02-13 20:17 10K 
[ ]out.DC_start 2021-02-13 20:17 9.7K 
[ ]out.DC_start.dat 2021-02-13 20:16 2.5K 
[TXT]out.DC_start_all 2021-02-13 20:17 11K 
[ ]out.DC_xray 2021-02-13 20:17 9.4K 
[ ]out.DC_xray.dat 2021-02-13 20:16 2.4K 
[TXT]out.DC_xray_all 2021-02-13 20:16 13K 
[TXT]out.DC_xray_info 2021-02-13 20:16 11K 
[TXT]out.buildpsf 2021-02-13 20:17 6.9K 
[ ]pixj_pcb.psf 2021-02-13 20:16 465K 
[ ]pixj_pcb_flex.psf 2021-02-13 20:17 465K 
[ ]rmsd.tcl 2021-02-13 20:18 1.1K 
[ ]rmsd_out_DC.tcl 2021-02-13 20:17 1.4K 
[TXT]start.pdb 2021-02-13 20:17 206K 
[TXT]xray.pdb 2021-02-13 20:17 92K 
[ ]xray.pse 2021-02-13 20:16 699K 
[TXT]xray_h.pdb 2021-02-13 20:17 181K 
[TXT]xray_h_build.pdb 2021-02-13 20:16 204K 
[TXT]xray_h_molmol.pdb 2021-02-13 20:16 181K 

- 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!