Bad sheet data

[wolfram.seifert@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
After using ISOLDE to improve my structure and save using the following command line:
isolde write phenixRsrInput #1.2 2.4 #1.1 modelFileName TauB_refinement5_one_nucleotide_fixed.cif paramFileName TauB_refinement5_one_nucleotide_fixed.eff
I got the following error and the regions that are not modelled in my structure now are filled with a line from the starting point of this region till the end of it.
Bad sheet data. Please use Help / Report a Bug with this structure.


Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/maps/W5_J202_localresolution.mrc

Opened W5_J202_localresolution.mrc as #1, grid size 320,320,320, pixel 0.822,
shown at level 0.128, step 2, values float32  

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement3/TauA_DNA_refinement2_ready_for_phenix_real_space_refined_000.cif

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement3/TauA_DNA_refinement2_ready_for_phenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 294  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "18" near line 113  
Bad residue range for struct_conf "19" near line 114  
Bad residue range for struct_conf "20" near line 115  
Bad residue range for struct_conf "21" near line 116  
Bad residue range for struct_conf "22" near line 117  
24 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for
TauA_DNA_refinement2_ready_for_phenix_real_space_refined_000.cif #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> volume #1 step 1

> select add #2

12264 atoms, 12711 bonds, 108 pseudobonds, 1373 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> volume #1 level 0.2

> dssp

> dssp minStrandLen 2

> hide #!1 models

> color sel bychain

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement2/TauA_DNA_emergencystructure.pdb

Chain information for TauA_DNA_emergencystructure.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> select subtract #2

Nothing selected  

> select add #3

12269 atoms, 12716 bonds, 1374 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!2 models

> show #!2 models

> select subtract #3

Nothing selected  

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1/TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1/TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 159  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "13" near line 106  
Bad residue range for struct_conf "14" near line 107  
Bad residue range for struct_conf "15" near line 108  
Bad residue range for struct_conf "16" near line 109  
Bad residue range for struct_conf "17" near line 110  
29 messages similar to the above omitted  
Invalid residue range for struct_conf "56": invalid chain "E", near line 149  
Invalid residue range for struct_conf "57": invalid chain "E", near line 150  
Invalid residue range for struct_conf "58": invalid chain "E", near line 151  
Invalid residue range for struct_conf "59": invalid chain "E", near line 152  
Invalid residue range for struct_conf "60": invalid chain "E", near line 153  
4 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for
TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif
#4  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> dssp minStrandLen 2

> hide #!3 models

> hide #!2 models

> color #!4 bychain

> hide #!4 models

> show #!3 models

> show #!4 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> close #4

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> close #3

> close #1

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/maps/W5_J202_localresolution.mrc

Opened W5_J202_localresolution.mrc as #1, grid size 320,320,320, pixel 0.822,
shown at level 0.128, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.1419

> volume #1 level 0.2

> volume #1 level 0.1459

> volume #1 level 0.2203

> select #2/E.F

Expected an objects specifier or a keyword  

> select #2/E,F

1845 atoms, 2068 bonds, 108 pseudobonds, 90 residues, 2 models selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 1845 atom styles  

> select #2/E:1-6,40-45,D:1-6,39-45

259 atoms, 287 bonds, 13 residues, 1 model selected  

> select #2/E:1-6,40-45/D:1-6,39-45

338 atoms, 363 bonds, 25 residues, 1 model selected  

> select #2/E:1-6,40-45/F:1-6,39-45

511 atoms, 569 bonds, 28 pseudobonds, 25 residues, 2 models selected  

> select #2/E:1-6,40-45/F:1-6,40-45

492 atoms, 548 bonds, 28 pseudobonds, 24 residues, 2 models selected  

> delete sel

> cd
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement3

Current working directory is:
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauA\Eustermann_method\J202_37Amap\Isolde_Alphafold_method\Refinement3  

> save
> TauA_DNA_refinement2_ready_for_phenix_real_space_refined_000_DNAtest.pdb #2

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1/TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1/TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 159  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "13" near line 106  
Bad residue range for struct_conf "14" near line 107  
Bad residue range for struct_conf "15" near line 108  
Bad residue range for struct_conf "16" near line 109  
Bad residue range for struct_conf "17" near line 110  
29 messages similar to the above omitted  
Invalid residue range for struct_conf "56": invalid chain "E", near line 149  
Invalid residue range for struct_conf "57": invalid chain "E", near line 150  
Invalid residue range for struct_conf "58": invalid chain "E", near line 151  
Invalid residue range for struct_conf "59": invalid chain "E", near line 152  
Invalid residue range for struct_conf "60": invalid chain "E", near line 153  
4 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for
TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000.cif
#3  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> hide #!2 models

> hide #!1 models

> dssp

> show #!1 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> hide #!1 models

> show #!3 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> transparency

Missing or invalid "percent" argument: Expected a number  

> transparency 50

> graphics silhouettes true

> lighting soft

> select #3/E:1-258

1977 atoms, 2033 bonds, 244 residues, 1 model selected  

> delete sel

> cd
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/Isolde_Alphafold_method/Refinement1

Current working directory is:
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauA\Eustermann_method\J202_37Amap\Isolde_Alphafold_method\Refinement1  

> save
> TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000_deletedPhosphatasedomain.pdb
> #3

> select #3/B

3483 atoms, 3548 bonds, 428 residues, 1 model selected  

> select #3/B:108-239

1106 atoms, 1127 bonds, 132 residues, 1 model selected  

> delete sel

> select #3/D:17-39

174 atoms, 178 bonds, 23 residues, 1 model selected  

> select #3/D:17-34

134 atoms, 137 bonds, 18 residues, 1 model selected  

> color sel bychain

> hide #!3 models

> show #!3 models

> select add #3

7390 atoms, 7538 bonds, 914 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select subtract #3.1

Nothing selected  

> color #!3 bychain

> select #3/D:17-34

134 atoms, 137 bonds, 18 residues, 1 model selected  

> delete sel

> save
> TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000_deletedPhosphatasedomain_deletedHelical_deletedt95Nterminus.pdb
> #3

Cannot save
'TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000_deletedPhosphatasedomain_deletedHelical_deletedt95Nterminus.pdb':
Unable to open file
'TauA_trimmered_Alphafold_Isolde_refinement_1_for_phenix_real_space_refined_000_deletedPhosphatasedomain_deletedHelical_deletedt95Nterminus.pdb'
for writing  

> save
> TauA_refinement_deletedPhosphatasedomain_deletedHelical_deletedt95Nterminus.pdb
> #3

> volume #1 level 0.3284

> select #3/C:17-34

Nothing selected  

> select #3/C:732-777

385 atoms, 393 bonds, 46 residues, 1 model selected  

> select #3/C:732-771

334 atoms, 341 bonds, 40 residues, 1 model selected  

> delete sel

> volume #1 level 0.35

> select #3/B:431-443

100 atoms, 99 bonds, 13 residues, 1 model selected  

> delete sel

> hide pseudobonds

> select #3/D:248-252

41 atoms, 42 bonds, 5 residues, 1 model selected  

> delete sel

> select #3/B:366-371

39 atoms, 38 bonds, 6 residues, 1 model selected  

> delete sel

> select #3/B:403-416

126 atoms, 128 bonds, 14 residues, 1 model selected  

> delete sel

> select #3/C:852-864

95 atoms, 94 bonds, 13 residues, 1 model selected  

> delete sel

> select #3/E:413-419

58 atoms, 57 bonds, 7 residues, 1 model selected  

> delete sel

> save TauA_refinement_1_trimmered.pdb #3

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauA/Eustermann_method/J202_37Amap/maps/cryosparc_P43_J202_006_volume_map.mrc

Opened cryosparc_P43_J202_006_volume_map.mrc as #4, grid size 320,320,320,
pixel 0.822, shown at level 0.133, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.2218

> volume #4 level 0.3103

> hide #!1 models

> hide #!3 models

> volume #4 level 0.1619

> volume #4 level 0.2744

> close #3

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> set bgColor #ffffff00

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> color #1/D:12-23/E:52-63 #7BBCD4

> color #1/I:12-23/J:52-63 #7BBCD4

> open 8CLI

Summary of feedback from opening 8CLI fetched from pdb  
---  
note | Fetching compressed mmCIF 8cli from
http://files.rcsb.org/download/8cli.cif  
  
8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B hot pink

> color #2/C dark salmon

> color #2/D,E cornflower blue

> color #2/D:16-26/E:15-25 #7BBCD4

> color #1/A:174-251 dark khaki

> color #1/A:252-337 medium aquamarine

> color #1/A:367-437 pale green

> color #1/A:610-714 peru

> color #1/D:12-23/E:52-63 #7BBCD4

> color #1/I:12-23/J:52-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> ui mousemode right "move picked models"

> view matrix models #2,1,0,0,9.9226,0,1,0,24.621,0,0,1,23.909

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> view matrix models #2,1,0,0,3.8688,0,1,0,12.837,0,0,1,82.529

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> color #1/D:12-23/E:52-63 #7BBCD4

> color #1/I:12-23/J:52-63 #7BBCD4

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-23/E:52-63 #7BBCD4

> color #2/I:12-23/J:52-63 #7BBCD4

> graphics silhouettes true

> turn

> cartoon

> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20

> cartoon style ~(nucleic|strand) xsection round

> cartoon style (nucleic|strand) xsection rectangle

> cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6

> cartoon style nucleic xsection round width 2 thickness 0.4

> hide pseudobonds

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,7.878,0,1,0,-26.23,0,0,1,76.007

> view matrix models #2,1,0,0,-11.628,0,1,0,36.992,0,0,1,-110.99

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.5306,-0.78095,0.32951,351.49,0.8162,-0.57561,-0.049919,200.68,0.22866,0.24246,0.94283,-187.81

> view matrix models
> #2,-0.81677,0.37717,-0.4366,372.48,-0.57508,-0.59317,0.56341,316.85,-0.046478,0.71126,0.70139,-166.01

> view matrix models
> #2,0.89101,-0.30795,-0.33356,153.08,-0.32579,-0.94544,0.002583,478.57,-0.31616,0.10637,-0.94272,416.3

> view matrix models
> #2,-0.0127,0.97523,0.22083,-63.336,0.89332,-0.088156,0.44069,-32.364,0.44924,0.20287,-0.87007,232.55

> view matrix models
> #2,-0.063644,0.97446,0.21537,-52.051,0.96206,0.0025385,0.27282,-21.122,0.2653,0.22456,-0.93765,280.52

> view matrix models
> #2,0.26042,-0.089172,-0.96137,388.75,0.95438,-0.12686,0.27029,6.246,-0.14606,-0.9879,0.052067,347.71

> view matrix models
> #2,0.32178,-0.90838,-0.26701,362.69,0.93868,0.26919,0.21543,-54.297,-0.12381,-0.31996,0.93931,-9.573

> ui mousemode right "move picked models"

> view matrix models
> #2,0.32178,-0.90838,-0.26701,366.6,0.93868,0.26919,0.21543,-74.593,-0.12381,-0.31996,0.93931,-14.546

> select subtract #2

Nothing selected  

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #2/D:12-23/E:52-63 #7BBCD4

> color #2/D,E cornflower blue

> color #2/D:12-23/E:52-63 #7BBCD4

> color #2/B dark salmon

> color #2/C hot pink

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.50912,-0.85937,-0.047769,266.11,0.83753,0.48185,0.25762,-107.31,-0.19837,-0.17117,0.96507,-35.768

> select subtract #2

Nothing selected  

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,6.4353,0,1,0,-35.571,0,0,1,105.96

> view matrix models
> #2,0.50912,-0.85937,-0.047769,267.05,0.83753,0.48185,0.25762,-100.54,-0.19837,-0.17117,0.96507,-53.322

> ui mousemode right "rotate selected models"

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> view matrix models
> #2,0.44933,-0.81697,-0.36147,348.94,0.094702,0.44589,-0.89006,336.82,0.88833,0.3657,0.27772,-193.93

> view matrix models
> #2,0.42489,-0.82246,-0.37819,358.89,-0.024891,0.407,-0.91309,373.11,0.9049,0.39738,0.15246,-171.86

> select subtract #2

Nothing selected  

> select add #1

15002 atoms, 15478 bonds, 97 pseudobonds, 1747 residues, 2 models selected  

> view matrix models
> #1,0.89759,-0.049527,-0.43805,126.53,-0.43638,0.041047,-0.89882,431.01,0.062497,0.99793,0.015231,91.106

> select subtract #1

Nothing selected  

> ui mousemode right "move picked models"

> view matrix models
> #1,0.89759,-0.049527,-0.43805,125.27,-0.43638,0.041047,-0.89882,416.7,0.062497,0.99793,0.015231,110.8

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.43689,-0.82036,-0.36897,353.87,0.043174,0.42884,-0.90235,353.11,0.89848,0.3783,0.22278,-184.55

> view matrix models
> #2,0.66092,-0.54187,-0.5192,294.26,-0.063366,0.64908,-0.75808,294.33,0.74778,0.53393,0.39465,-229.17

> view matrix models
> #2,0.65957,-0.54218,-0.52059,294.93,-0.070903,0.64463,-0.7612,297.43,0.74829,0.53897,0.38674,-228.27

> view matrix models
> #2,0.67833,-0.60729,-0.41361,277.2,-0.024673,0.54377,-0.83887,327.75,0.73435,0.57923,0.35387,-225.21

> ui mousemode right "move picked models"

> view matrix models
> #2,0.67833,-0.60729,-0.41361,279.68,-0.024673,0.54377,-0.83887,336.71,0.73435,0.57923,0.35387,-217.36

> select subtract #2

Nothing selected  

> select add #1

15002 atoms, 15478 bonds, 97 pseudobonds, 1747 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.89847,-0.046385,-0.43657,124.15,-0.43443,0.04959,-0.89934,414.67,0.063365,0.99769,0.024404,108.8

> view matrix models
> #1,0.89429,-0.061344,-0.44326,129.41,-0.44357,0.0092854,-0.89619,424.08,0.059092,0.99807,-0.018906,118.45

> view matrix models
> #1,0.76824,0.071463,-0.63616,166.25,-0.64006,0.068662,-0.76525,423.17,-0.011007,0.99508,0.09849,108.57

> select subtract #1

Nothing selected  

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> view matrix models
> #2,0.69153,-0.60185,-0.39946,272.53,0.016661,0.56615,-0.82414,320.72,0.72216,0.56326,0.40153,-223.87

> ui mousemode right "move picked models"

> view matrix models
> #2,0.69153,-0.60185,-0.39946,269.78,0.016661,0.56615,-0.82414,313.96,0.72216,0.56326,0.40153,-225.17

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.68059,-0.60634,-0.41128,275.71,-0.017676,0.54759,-0.83656,327.28,0.73245,0.57662,0.36197,-219.83

> select subtract #2

Nothing selected  

> ui mousemode right "move picked models"

> view matrix models
> #1,0.76824,0.071463,-0.63616,163.66,-0.64006,0.068662,-0.76525,416.92,-0.011007,0.99508,0.09849,107.12

> ui mousemode right "move picked models"

> view matrix models
> #2,0.68059,-0.60634,-0.41128,280.52,-0.017676,0.54759,-0.83656,308.13,0.73245,0.57662,0.36197,-153.97

> ui mousemode right "rotate selected models"

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> view matrix models
> #2,0.62557,-0.63112,-0.45864,307.79,-0.1784,0.45657,-0.87162,365.49,0.7595,0.62708,0.17302,-121.6

> view matrix models
> #2,0.69258,-0.60142,-0.39828,274,0.020013,0.56794,-0.82283,293.48,0.72107,0.5619,0.40538,-159.81

> view matrix models
> #2,0.68294,-0.56001,-0.46901,285.51,-0.073114,0.58644,-0.80669,303.67,0.7268,0.58521,0.35956,-153.96

> ui mousemode right "move picked models"

> view matrix models
> #2,0.68294,-0.56001,-0.46901,283.41,-0.073114,0.58644,-0.80669,298.59,0.7268,0.58521,0.35956,-155.13

> select subtract #2

Nothing selected  

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.66009,-0.65879,-0.36095,279.95,0.021187,0.49664,-0.8677,313.36,0.75089,0.56511,0.34178,-151.37

> select subtract #2

Nothing selected  

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> view matrix models
> #2,0.68468,-0.54753,-0.48108,283.66,-0.084401,0.59605,-0.7985,296.82,0.72394,0.58732,0.36189,-155.58

> select subtract #2

Nothing selected  

> cd C:/Users/wseif/Desktop/Publication/yTFIIIC/Fig1

Current working directory is: C:\Users\wseif\Desktop\Publication\yTFIIIC\Fig1  

> save
> C:/Users/wseif/Desktop/Publication/yTFIIIC/Fig1/yeastTauB_humanTauB_DNAbindingcomparison.cxs
> includeMaps true

> ui mousemode right "move picked models"

> mmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8cli, chain A (#2) with
TauB_refinement5_for_fenix_real_space_refined_000.cif, chain A (#1), sequence
alignment score = 355  
RMSD between 47 pruned atom pairs is 1.251 angstroms; (across all 406 pairs:
14.798)  
  

> mmaker #1/A to #2/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8cli, chain A (#2) with
TauB_refinement5_for_fenix_real_space_refined_000.cif, chain A (#1), sequence
alignment score = 355  
RMSD between 47 pruned atom pairs is 1.251 angstroms; (across all 406 pairs:
14.798)  
  

> mmaker #1/A:108-172 to #2/A:174-251

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8cli, chain A (#2) with
TauB_refinement5_for_fenix_real_space_refined_000.cif, chain A (#1), sequence
alignment score = 82.6  
RMSD between 49 pruned atom pairs is 0.983 angstroms; (across all 65 pairs:
2.709)  
  

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> hide #!2 models

> show #!1 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> mmaker #1/ to #2/A:174-251

> matchmaker #1/ to #2/A:174-251

Missing required "to" argument  

> mmaker #1/D to #2/D

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8cli, chain D (#2) with
TauB_refinement5_for_fenix_real_space_refined_000.cif, chain D (#1), sequence
alignment score = 61.6  
RMSD between 14 pruned atom pairs is 1.114 angstroms; (across all 35 pairs:
3.979)  
  

> show #!2 models

> select add #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.59878,-0.79284,-0.11348,255.78,-0.2541,-0.32242,0.91186,79.485,-0.75954,-0.51716,-0.39451,534.15

> ui mousemode right "move picked models"

> view matrix models
> #1,0.89939,0.4192,0.12398,-102.88,-0.051407,-0.18021,0.98228,51.634,0.43411,-0.88983,-0.14053,312.9

> mmaker #1/D,E to #2/D,E

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8cli, chain E (#2) with
TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1), sequence
alignment score = 61.6  
RMSD between 15 pruned atom pairs is 1.138 angstroms; (across all 35 pairs:
3.962)  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.84918,0.22286,0.47879,186.39,0.48426,-0.033099,0.8743,-109.08,0.21069,0.97429,-0.079813,-21.927

> view matrix models
> #2,0.53298,0.3055,0.78905,-172.49,0.00070306,-0.9327,0.36064,288.1,0.84613,-0.19166,-0.49733,188.67

> view matrix models
> #2,0.61912,-0.7779,-0.10754,247.47,-0.30469,-0.36417,0.88008,105.31,-0.72378,-0.51211,-0.46249,543.36

> select subtract #2

Nothing selected  

> select add #1

15002 atoms, 15478 bonds, 97 pseudobonds, 1747 residues, 2 models selected  

> view matrix models
> #1,-0.69668,0.47505,0.53755,117.14,0.35846,-0.41856,0.83446,47.073,0.62141,0.77404,0.12131,-100.06

> view matrix models
> #1,0.91297,0.4027,0.065745,-83.894,0.051481,-0.27352,0.96049,51.036,0.40477,-0.87351,-0.27045,361.12

> ui mousemode right "move picked models"

> view matrix models
> #1,0.91297,0.4027,0.065745,-77.261,0.051481,-0.27352,0.96049,47.039,0.40477,-0.87351,-0.27045,333.5

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.86094,0.50695,-0.042157,-66.4,-0.037053,0.14514,0.98872,-27.589,0.50735,-0.84966,0.14374,223.55

> view matrix models
> #1,0.99368,-0.11135,-0.013889,29.051,0.012305,-0.014894,0.99981,-6.576,-0.11154,-0.99367,-0.013429,405.73

> view matrix models
> #1,0.99948,-0.032177,-0.0020105,9.2131,0.001278,-0.022767,0.99974,-2.7995,-0.032215,-0.99922,-0.022714,393.36

> mmaker #1/D:16-26/E:15-25 to #2/D:12-23/E:52-63

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8cli, chain E (#2) with
TauB_refinement5_for_fenix_real_space_refined_000.cif, chain D (#1), sequence
alignment score = 34.2  
RMSD between 11 pruned atom pairs is 0.762 angstroms; (across all 11 pairs:
0.762)  
  

> select subtract #1

Nothing selected  

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> close #2

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-23/E:52-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> mmaker #2/D:12-23/E:52-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> cartoon

> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20

> cartoon style ~(nucleic|strand) xsection round

> cartoon style (nucleic|strand) xsection rectangle

> cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6

> cartoon style nucleic xsection round width 2 thickness 0.4

> hide pseudobonds

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-23/E:52-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> mmaker #2/D:12-23/E:52-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> cartoon style width 1.5 thickness 0.3

> cartoon style helix width 1.5 thickness 0.3

> cartoon style strand xsection rectangle width 2

> hide #!2 models

> ribbon style x rect

> ribbon style (#1 & coil) x oval

> cartoon style protein modeHelix default arrows false xsection oval width 1
> thickness 1

> cartoon style protein modeHelix default arrows false xsection oval width 2
> thickness 2

> cartoon style protein modeHelix default arrows false xsection oval width 3
> thickness 3

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> select #2 transparency 60

Expected a keyword  

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 60

> hide #!1 models

> hide pseudobonds

> transparency 60

> transparency 60 sel cartoons

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> transparency sel cartoons 60

Missing or invalid "percent" argument: Expected a number  

> transparency sel 60 cartoons

> hide #!2 models

> show #!1 models

> show #!2 models

> select subtract #2

Nothing selected  

> transparency sel 50 cartoons

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 40 cartoons

> select subtract #2

Nothing selected  

> mmaker #2/B to #1/C

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain C (#1)
with 8cli, chain B (#2), sequence alignment score = 225.6  
RMSD between 94 pruned atom pairs is 1.161 angstroms; (across all 508 pairs:
10.994)  
  

> mmaker #2/C to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain B (#1)
with 8cli, chain C (#2), sequence alignment score = 328.6  
RMSD between 212 pruned atom pairs is 1.159 angstroms; (across all 454 pairs:
10.624)  
  

> hide #!2 models

> show #!2 models

> color #2 grey

> mmaker #2/D:12-23/E:52-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> nucleotides stubs

> cartoon

> cartoon style modeHelix default arrows true arrowsHelix false arrowScale 2
> width 2 thickness 0.4 sides 12 divisions 20

> cartoon style ~(nucleic|strand) xsection round

> cartoon style (nucleic|strand) xsection rectangle

> cartoon style protein modeHelix tube radius 2 sides 24 thickness 0.6

> cartoon style nucleic xsection round width 2 thickness 0.4

> hide pseudobonds

> cartoon style protein modeHelix default arrows false xsection oval width 3
> thickness 3

> close #2

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-23/E:52-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> mmaker #2/D:12-23/E:52-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> hide #!1 models

> mmaker #2/D:12-23/E:52-63

> matchmaker #2/D:12-23/E:52-63

Missing required "to" argument  

> select #2/D:12-23/E:52-63

492 atoms, 550 bonds, 32 pseudobonds, 24 residues, 2 models selected  
Alignment identifier is 2/D  
Alignment identifier is 2/E  

> show #!1 models

> close #1

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-22/E:53-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> cartoon style thickness 2.5

> lighting soft

> silhouette width 1.5

Unknown command: silhouette width 1.5  

> hide #!2 models

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> lighting soft

> silhouette width 0.5

Unknown command: silhouette width 0.5  

> graphics silhouettes false

> graphics silhouettes true

> silhouettes width 0.5

Unknown command: silhouettes width 0.5  

> graphics silhouettes width 0.5

> graphics silhouettes width 1.5

> graphics silhouettes width 2

> cartoon style thickness 2.5

> cartoon style thickness 1.5

> cartoon style thickness 3

> cartoon style thickness 2

> cartoon style thickness 2.5

> show #!2 models

> hide #!2 models

> close #2

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-22/E:53-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-22/E:53-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> select #2/B,C#3/B,C

10099 atoms, 10376 bonds, 13 pseudobonds, 1270 residues, 3 models selected  

> show #!2 models

> hide #!2 models

> select #2/B,C#1/B,C

19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected  

> show #!2 models

> hide #!2 models

> hide sel

> hide sel cartoons

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> select add #1

25101 atoms, 25854 bonds, 110 pseudobonds, 3017 residues, 5 models selected  

> select add #2

30957 atoms, 31946 bonds, 205 pseudobonds, 3629 residues, 6 models selected  

> select subtract #1

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> select subtract #2

Nothing selected  

> select clear

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 60 cartoons

> select clear

> hide pseudobonds

> show ribbons

> select #2/B,C#1/B,C

19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected  

> hide sel cartoons

> select clear

> cartoon style protein modeHelix tube radius 2 sides 24 vvvvvv

Expected a keyword  

> cartoon style protein modeHelix tube radius 2 sides 24

> hide #!2 models

> close #2

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-22/E:53-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> hide pseudobonds

> mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> select #2/B,C#1/B,C

19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected  

> hide sel cartoons

> select clear

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 60 cartoons

> select clear

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 40 cartoons

> select clear

> view

> view matrix

view matrix camera
-0.24397,0.003917,-0.96977,-160.33,0.26193,-0.96256,-0.069782,168.08,-0.93374,-0.27104,0.23381,293.51  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view matrix models
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0

[Repeated 2 time(s)]

> view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0

> view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0l

Invalid "models" argument: Require numeric values  

> view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0

> view initial #1

> view position mod
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0

Missing or invalid "models" argument: invalid models specifier  

> view position
> #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0

Missing or invalid "models" argument: only initial part
"#1,1,0,0,0,0,1,0,0,0,0,1,0" of atom specifier valid  

> view matrix models #1

Invalid "models" argument: Expected model id and 12 comma-separated numbers  

> view matrix models #1

Invalid "models" argument: Expected model id and 12 comma-separated numbers  

> view matrix models #1

Invalid "models" argument: Expected model id and 12 comma-separated numbers  

> view matrix

view matrix camera
-0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0  
  

>
> -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42

Unknown command:
-0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42  

> view
> -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42

Expected an objects specifier or a view name or a keyword  

> view matrix
> -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42

Expected a keyword  

> view matrix camera
> -0.38389,0.080464,-0.91987,-102.07,0.19585,-0.96644,-0.16627,142.22,-0.90237,-0.24398,0.35525,318.42

[Repeated 2 time(s)]

> view matrix

view matrix camera
-0.33132,0.081403,-0.94,12.509,0.24498,-0.95469,-0.16902,163.33,-0.91116,-0.28627,0.29637,273.03  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view matrix camera
> -0.33132,0.081403,-0.94,12.509,0.24498,-0.95469,-0.16902,163.33,-0.91116,-0.28627,0.29637,273.03

> hide #!2 models

> select #1/A:1-107,173-668#2/A:1-173,252-714

7676 atoms, 7788 bonds, 4 pseudobonds, 946 residues, 3 models selected  

> hide sel cartoons

> select clear

> show #!2 models

> select #1/A:1-107,173-668#2/A:1-173,252-715

7682 atoms, 7794 bonds, 4 pseudobonds, 947 residues, 3 models selected  

> hide sel cartoons

> select clear

> select clearcccselect #1/A:1-107,173-668#2/A:1-173,252-716

Expected an objects specifier or a keyword  

> hide sel cartoons

> select clear

> select #1/A:1-107,173-668#2/A:1-173,252-716

7690 atoms, 7802 bonds, 4 pseudobonds, 948 residues, 3 models selected  

> hide sel cartoons

> select clear

> hide #!2 models

> show #!2 models

> color #2/A:174-251 grey

> select #1/A:1-107,173-668#2/A:1-173,252-716/D,E

9125 atoms, 9410 bonds, 95 pseudobonds, 1018 residues, 4 models selected  

> hide sel cartoons

> select clear

> select #1/A:1-107,173-668#2/A:1-173,252-716/D,E

9125 atoms, 9410 bonds, 95 pseudobonds, 1018 residues, 4 models selected  

> hide sel cartoons

> hide atoms

> select clear

> select #1/D,E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> select add #1

15002 atoms, 15478 bonds, 97 pseudobonds, 1747 residues, 2 models selected  

> select cleaer

Expected an objects specifier or a keyword  

> select clear

> select #1/A:1-107,173-668/D:1-14,32-40/E:1-11,27-40#2/A:1-173,252-716/D,E

10108 atoms, 10509 bonds, 152 pseudobonds, 1066 residues, 5 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> view matrix

view matrix camera
-0.24482,-0.01464,-0.96946,53.443,0.27457,-0.96001,-0.05484,185.79,-0.92988,-0.2796,0.23905,254.21  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0  
  

> view matrix

view matrix camera
-0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0  
  

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-22/E:53-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> hide pseudobonds

> mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> select #2/B,C#1/B,C

19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected  

> hide sel cartoons

> select clear

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 40 cartoons

> select clear

> Focus on th Wh2 domain

Unknown command: Focus on th Wh2 domain  

>
> -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83

Unknown command:
-0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83  

> let's hide the other domains and DNA

Unknown command: let's hide the other domains and DNA  

> select #1/A:1-107,173-668/D:1-14,32-40/E:1-11,27-40#2/A:1-173,252-716/D,E

10108 atoms, 10509 bonds, 152 pseudobonds, 1066 residues, 5 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> color #2/A:174-251 grey

> view matrix
> -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83

Expected a keyword  

> view matrix camera
> -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-22/E:53-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> hide pseudobonds

> mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> select #2/B,C#1/B,C

19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected  

> hide sel cartoons

> select clear

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 40 cartoons

> select clear

> view matrix camera
> -0.1951,-0.078669,-0.97762,57.479,0.25808,-0.96578,0.02621,197.21,-0.94622,-0.24718,0.20873,248.83

> let's hide the other domains and DNA

Unknown command: let's hide the other domains and DNA  

> select #1/A:1-107,173-668/D:1-14,32-40/E:1-11,27-40#2/A:1-173,252-716/D,E

10108 atoms, 10509 bonds, 152 pseudobonds, 1066 residues, 5 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> color #2/A:174-251 grey

> cd
> C:/Users/wseif/Desktop/Publication/yTFIIIC/Fig_comparison_yeast_human_TauB_DNA_interactions

Current working directory is:
C:\Users\wseif\Desktop\Publication\yTFIIIC\Fig_comparison_yeast_human_TauB_DNA_interactions  

> save WH2_zoomin_comparison_WS_01.png width 7200 transparentBackground true

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-22/E:53-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> hide pseudobonds

> mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> select #2/B,C#1/B,C

19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected  

> hide sel cartoons

> select clear

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 40 cartoons

> select clear

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> view matrix

view matrix camera
-0.40992,-0.71131,-0.57097,119.39,0.50216,-0.69857,0.50974,254.91,-0.76145,-0.077771,0.64355,338.88  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0  
  

> hide #!2 models

> view matrix camera
> -0.40992,-0.71131,-0.57097,119.39,0.50216,-0.69857,0.50974,254.91,-0.76145,-0.077771,0.64355,338.88

> select #1/A:1-184,262-668/D:1-24/E:16-40#2/A:1-251,338-716/D,E

10049 atoms, 10463 bonds, 148 pseudobonds, 1060 residues, 5 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> show #!2 models

> hide #!2 models

> color #2/A:252-337 grey

> show #!2 models

> show #1/E:16

> show #1/E:16 cartoons

> show #1/E:16-20 cartoons

> show #1/D:22-25 cartoons

> show #1/D:22-25 atoms

> show #1/E:16-20 atoms

> show #1/D:22-25 atoms

> show #1/D:21-25 atoms

> show #1/D:21-25 cartoons

> view matrix

view matrix camera
-0.36384,-0.71791,-0.59348,105.42,0.076066,-0.65793,0.74923,300.71,-0.92835,0.22745,0.294,291.68  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0  
  

> save WH3_zoomin_comparison_WS_01.png width 7200 transparentBackground true

> close #2

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-22/E:53-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> hide pseudobonds

> mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> select #2/B,C#1/B,C

19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected  

> hide sel cartoons

> select clear

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 40 cartoons

> select clear

> view matrix

view matrix camera
-0.34791,0.044606,-0.93646,-123.99,0.30379,-0.93961,-0.15762,142.25,-0.88694,-0.33933,0.31335,313.94  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0  
  

> close

> open
> C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5\TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> open 8CLI

8cli title:  
TFIIIC TauB-DNA monomer [more info...]  
  
Chain information for 8cli #2  
---  
Chain | Description | UniProt  
A | General transcription factor 3C polypeptide 1 | TF3C1_HUMAN 1-2109  
B | General transcription factor 3C polypeptide 4 | TF3C4_HUMAN 1-822  
C | General transcription factor 3C polypeptide 2 | TF3C2_HUMAN 1-911  
D | DNA (35-MER) |  
E | DNA (35-MER) |  
  
Non-standard residues in 8cli #2  
---  
ZN — zinc ion  
  

> dssp minStrandLen 2

> color #2/A forest green

> color #2/B dark salmon

> color #2/C hot pink

> color #2/D,E cornflower blue

> color #2/A:174-251 dark khaki

> color #2/A:252-337 medium aquamarine

> color #2/A:367-437 pale green

> color #2/A:610-714 peru

> color #2/D:12-22/E:53-63 #7BBCD4

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #2/D-E

1435 atoms, 1608 bonds, 91 pseudobonds, 70 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1435 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> hide pseudobonds

> mmaker #2/D:12-22/E:53-63 to #1/D:16-26/E:15-25

Using Nucleic matrix instead of BLOSUM-62 for matching  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | Nucleic  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker TauB_refinement5_for_fenix_real_space_refined_000.cif, chain E (#1)
with 8cli, chain D (#2), sequence alignment score = 34.2  
RMSD between 10 pruned atom pairs is 0.815 angstroms; (across all 11 pairs:
1.244)  
  

> select #2/B,C#1/B,C

19039 atoms, 19522 bonds, 13 pseudobonds, 2388 residues, 4 models selected  

> hide sel cartoons

> select clear

> select #2

15955 atoms, 16468 bonds, 108 pseudobonds, 1882 residues, 4 models selected  

> transparency sel 40 cartoons

> select clear

> view matrix camera
> -0.34791,0.044606,-0.93646,-123.99,0.30379,-0.93961,-0.15762,142.25,-0.88694,-0.33933,0.31335,313.94

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select #1/A:1-333,417-668/D:1-13,28-40/E:1-13,28-40#2/A:1-366,438-716/D,E

10080 atoms, 10494 bonds, 160 pseudobonds, 1059 residues, 5 models selected  

> hide sel cartoons

> hide sel atoms

> select clear

> color #2/A:367-437 grey

> show #!2 models

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/W6_J290_monomer_localresolution.mrc

Opened W6_J290_monomer_localresolution.mrc as #3, grid size 480,480,480, pixel
0.822, shown at level 0.0492, step 2, values float32  

> volume #3 step 1

> volume #3 level 1.351

> transparency 60

> volume #3 level 0.5833

> volume #3 level 1.251

> volume #3 level 1.017

> hide #!3 models

> show #!3 models

> hide #!3 models

> view matrix

view matrix camera
0.014841,0.2777,0.96055,330.44,-0.41972,-0.8702,0.25806,213.9,0.90753,-0.40699,0.10364,221.52  
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.44617,-0.89391,0.043179,275.83,0.84557,0.43687,0.30684,-124.87,-0.29315,-0.10039,0.95078,34.481,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0,#2.3,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0  
  

> close #3

> close

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/W6_J290_monomer_localresolution.mrc

Opened W6_J290_monomer_localresolution.mrc as #2, grid size 480,480,480, pixel
0.822, shown at level 0.0492, step 2, values float32  

> clipper associate #2 toModel #1

Opened W6_J290_monomer_localresolution.mrc as #1.1.1.1, grid size 480,480,480,
pixel 0.822, shown at level 1.14, step 1, values float32  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  

> volume #1.1.1.1 level 0.8469

> close

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> set bgColor white

> lighting soft intensity 0.1 fillIntensity 0.5 ambientIntensity 1

> hide atoms

> show ribbons

> dssp minStrandLen 2

> cartoon style thickness 2.5

> graphics silhouettes width 1.5

> color #1/A forest green

> color #1/B hot pink

> color #1/C dark salmon

> color #1/D,E cornflower blue

> color #1/D:16-26/E:15-25 #7BBCD4

> color #1/A:108-172 dark khaki

> color #1/A:185-262 medium aquamarine

> color #1/A:334-416 pale green

> color #1/A:550-640 peru

> select #1/D-E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> show sel atoms

> style sel stick

Changed 1640 atom styles  

> show sel atoms

> nucleotides sel tube/slab shape muffler

> select clear

> close

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif

Summary of feedback from opening
C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 268  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "25" near line 119  
Bad residue range for struct_conf "26" near line 120  
Bad residue range for struct_conf "32" near line 126  
Bad residue range for struct_conf "33" near line 127  
Bad residue range for struct_conf "34" near line 128  
1 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/W6_J290_monomer_localresolution.mrc

Opened W6_J290_monomer_localresolution.mrc as #2, grid size 480,480,480, pixel
0.822, shown at level 0.0492, step 2, values float32  

> clipper associate #2 toModel #1

Opened W6_J290_monomer_localresolution.mrc as #1.1.1.1, grid size 480,480,480,
pixel 0.822, shown at level 1.14, step 1, values float32  
Chain information for TauB_refinement5_for_fenix_real_space_refined_000.cif  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
1.2/E | No description available  
  

> select #1/D

817 atoms, 916 bonds, 40 residues, 1 model selected  

> 16

Unknown command: 16  

> select #1/D

817 atoms, 916 bonds, 40 residues, 1 model selected  

> 16view sel

Unknown command: 16view sel  

> view sel

> select #1/D:16

21 atoms, 23 bonds, 1 residue, 1 model selected  

> view sel

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 66 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> isolde restrain basepairs sel

> select #1/D,E

1640 atoms, 1838 bonds, 97 pseudobonds, 80 residues, 2 models selected  

> isolde sim start /D-E

Sim termination reason: None  
ISOLDE: stopped sim  

> addh #1.2

Summary of feedback from adding hydrogens to
TauB_refinement5_for_fenix_real_space_refined_000.cif #1.2  
---  
warnings | Not adding hydrogens to /D DA 1 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /E DG 1 P because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for
TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain A; guessing
termini instead  
No usable SEQRES records for
TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain B; guessing
termini instead  
No usable SEQRES records for
TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain C; guessing
termini instead  
No usable SEQRES records for
TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain D; guessing
termini instead  
No usable SEQRES records for
TauB_refinement5_for_fenix_real_space_refined_000.cif (#1.2) chain E; guessing
termini instead  
Chain-initial residues that are actual N termini: /A MET 1, /B SER 156, /C MET
1  
Chain-initial residues that are not actual N termini: /A VAL 322, /A LYS 538  
Chain-final residues that are actual C termini: /A ARG 668, /B SER 685, /C MET
588  
Chain-final residues that are not actual C termini: /A ILE 262, /A SER 477  
1716 hydrogen bonds  
Adding 'H' to /A VAL 322  
Adding 'H' to /A LYS 538  
14315 hydrogens added  
  

> isolde sim start /D-E

ISOLDE: started sim  

> select #1/D:16

32 atoms, 34 bonds, 1 residue, 1 model selected  

> isolde stepto /D:21

> isolde stepto next

[Repeated 3 time(s)]

> volume #1.1.1.1 level 0.5526

> volume #1.1.1.1 level 0.8697

> volume #1.1.1.1 level 0.6861

> volume #1.1.1.1 level 0.9198

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> select #1/D:16

32 atoms, 34 bonds, 1 residue, 1 model selected  

> view sel

> cd
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5

Current working directory is:
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5  

> isolde write phenixRsrInput #1.2 2.4 #1.1 modelFileName
> TauB_refinement5_one_nucleotide_fixed.cif paramFileName
> TauB_refinement5_one_nucleotide_fixed.eff

> dssp #1.2

> save TauB_refinement5_one_nucleotide_fixed.cif #1.2 selectedOnly true
> bestGuess true computedSheets true

The `computedSheets true` option requires the `pprintpp` module to be
installed, but this is missing in the ChimeraX 1.7 release. Use the command:  
pip install pprintpp  
on the ChimeraX command line to install it, then try again.  

> pip install pprintpp

> open
> C:/Users/wseif/Desktop/Cryosparc/230211_Merged_5_datasets/Refinement/TauB_Monomer/W6_J290/Refinement5/TauB_refinement5_one_nucleotide_fixed.cif

Chain information for TauB_refinement5_one_nucleotide_fixed.cif #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> hide #!1 models

> hide #!1.1 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> hide #1.3 models

> hide #!2 atoms

> show #!2 cartoons

> close #2

> hide #!1 models

> show #!1 models

> show #!1.2 models

> show #1.3 models

> show #!1.1 models

> save test.pdb #1.2

> isolde write phenixRsrInput #1.2 2.4 #1.1 modelFileName
> TauB_refinement5_one_nucleotide_fixed.cif paramFileName
> TauB_refinement5_one_nucleotide_fixed.eff

> dssp #1.2

> save TauB_refinement5_one_nucleotide_fixed.cif #1.2 selectedOnly true
> bestGuess true computedSheets true

Bad sheet data. Please use Help / Report a Bug with this structure.  

A phenix.real_space_refine input file
TauB_refinement5_one_nucleotide_fixed.eff with settings recommended for ISOLDE
models has been written to
C:\Users\wseif\Desktop\Cryosparc\230211_Merged_5_datasets\Refinement\TauB_Monomer\W6_J290\Refinement5
along with a current snapshot of your model
(TauB_refinement5_one_nucleotide_fixed.cif). You can start a refinement job by
running the following command in the working directory:  
phenix.real_space_refine TauB_refinement5_one_nucleotide_fixed.eff.  




OpenGL version: 3.3.0 NVIDIA 532.09
OpenGL renderer: NVIDIA GeForce RTX 2070 Super/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_DE.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Alienware
Model: Alienware m15 R3
OS: Microsoft Windows 11 Home (Build 22621)
Memory: 16,929,841,152
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10750H CPU @ 2.60GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.3
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    pprintpp: 0.4.0
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    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1
File attachment: TauB_refinement5_one_nucleotide_fixed.cif

TauB_refinement5_one_nucleotide_fixed.cif​

[wolfram.seifert@…]

Added by email2trac

[pett]

Hi Wolfram,

Thanks for reporting this problem. It got fixed a few days ago so if you get the 1.8 daily build you will be able to save your file without error. It will also be fixed in the 1.7.1 release, which we are hoping to make sometime in early January.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[wolfram.seifert@…]

Dear Eric,

Thanks for taking the time and reply my issue. Have a nice day.

Best,

Wolfram
On Thu, Dec 28, 2023 at 19:49, ChimeraX  wrote:
#10411: Bad sheet data
----------------------------------------+--------------------
Reporter:  wolfram.seifert@…  |      Owner:  pett
Type:  defect             |     Status:  closed
Priority:  normal             |  Milestone:
Component:  Input/Output       |    Version:
Resolution:  duplicate          |   Keywords:
Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
Project:  ChimeraX           |
----------------------------------------+--------------------
Changes (by pett):

* resolution:   => duplicate
* status:  accepted => closed

Comment:

Hi Wolfram,
Thanks for reporting this problem.  It got fixed a few days ago so
if you get the 1.8 daily build you will be able to save your file without
error.  It will also be fixed in the 1.7.1 release, which we are hoping to
make sometime in early January.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab