wiki:TracQuery

Trac Ticket Queries

Table of Contents

In addition to reports, Trac provides support for custom ticket queries, which can be used to display tickets that meet specified criteria.

To configure and execute a custom query, switch to the View Tickets module from the navigation bar, and select the Custom Query link.

Filters

When you first go to the query page, the default filter will display tickets relevant to you:

  • If logged in then all open tickets, it will display open tickets assigned to you.
  • If not logged in but you have specified a name or email address in the preferences, then it will display all open tickets where your email (or name if email not defined) is in the CC list.
  • If not logged in and no name/email is defined in the preferences, then all open issues are displayed.

Current filters can be removed by clicking the button to the left with the minus sign on the label. New filters are added from the pulldown lists at the bottom corners of the filters box; 'And' conditions on the left, 'Or' conditions on the right. Filters with either a text box or a pulldown menu of options can be added multiple times to perform an Or on the criteria.

You can use the fields just below the filters box to group the results based on a field, or display the full description for each ticket.

After you have edited your filters, click the Update button to refresh your results.

Some shortcuts can be used to manipulate checkbox filters.

  • Clicking on a filter row label toggles all checkboxes.
  • Pressing the modifier key while clicking on a filter row label inverts the state of all checkboxes.
  • Pressing the modifier key while clicking on a checkbox selects the checkbox and deselects all other checkboxes in the filter.

The modifier key is platform and browser dependent. On Mac the modified key is Option/Alt or Command. On Linux the modifier key is Ctrl + Alt. Opera on Windows seems to use Ctrl + Alt, while Alt is effective for other Windows browsers.

Clicking on one of the query results will take you to that ticket. You can navigate through the results by clicking the Next Ticket or Previous Ticket links just below the main menu bar, or click the Back to Query link to return to the query page.

You can safely edit any of the tickets and continue to navigate through the results using the Next/Previous/Back to Query links after saving your results. When you return to the query any tickets which were edited will be displayed with italicized text. If one of the tickets was edited such that it no longer matches the query criteria , the text will also be greyed. Lastly, if a new ticket matching the query criteria has been created, it will be shown in bold.

The query results can be refreshed and cleared of these status indicators by clicking the Update button again.

Saving Queries

Trac allows you to save the query as a named query accessible from the reports module. To save a query ensure that you have Updated the view and then click the Save query button displayed beneath the results. You can also save references to queries in Wiki content, as described below.

Note: one way to easily build queries like the ones below, you can build and test the queries in the Custom report module and when ready - click Save query. This will build the query string for you. All you need to do is remove the extra line breaks.

Note: you must have the REPORT_CREATE permission in order to save queries to the list of default reports. The Save query button will only appear if you are logged in as a user that has been granted this permission. If your account does not have permission to create reports, you can still use the methods below to save a query.

You may want to save some queries so that you can come back to them later. You can do this by making a link to the query from any Wiki page. 

[query:status=new|assigned|reopened&version=1.0 Active tickets against 1.0]

Which is displayed as:

Active tickets against 1.0

This uses a very simple query language to specify the criteria, see Query Language.

Alternatively, you can copy the query string of a query and paste that into the Wiki link, including the leading ? character: 

[query:?status=new&status=assigned&status=reopened&group=owner Assigned tickets by owner]

Which is displayed as:

Assigned tickets by owner

Customizing the table format

You can also customize the columns displayed in the table format (format=table) by using col=<field>. You can specify multiple fields and what order they are displayed in by placing pipes (|) between the columns: 

[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter)]]

This is displayed as:

Results (1 - 3 of 13671)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#20137 duplicate Crash on Mac waking from sleep Eric Pettersen bhogeba@…
#20136 duplicate Crash on Mac waking from sleep Eric Pettersen taic@…
#20135 duplicate Crash on Mac waking from sleep Tom Goddard taic@…
1 2 3 4 5 6 7 8 9 10 11 →

Full rows

In table format you can also have full rows by using rows=<field>: 

[[TicketQuery(max=3,status=closed,order=id,desc=1,format=table,col=resolution|summary|owner|reporter,rows=description)]]

This is displayed as:

Results (1 - 3 of 13671)

1 2 3 4 5 6 7 8 9 10 11 →
Ticket Resolution Summary Owner Reporter
#20137 duplicate Crash on Mac waking from sleep Eric Pettersen bhogeba@…
Description 
The following bug report has been submitted:
Platform:        macOS-26.3.1-arm64-arm-64bit
ChimeraX Version: 1.10rc202506100450 (2025-06-10 04:50:02 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Current thread 0x0000000206eff100 (most recent call first):
 File "/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
 File "/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
 File "/Applications/ChimeraX-1.10-rc2025.06.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 in 
 File "", line 88 in _run_code
 File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, psutil._psutil_osx, psutil._psutil_posix, chimerax.surface._surface, chimerax.map._map, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.atomic._ribbons, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._imagingmath, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 61)


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===== Log before crash start =====
UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/bhogeba/T4_dimeric
> tRNA/Ecoli_M1RNP/3'UAA_T4_tRNA/M1_Holo_T4dimer_ternary/Intermediates_and
> active conformer_publication.cxs"

Opened cryosparc_P23_J2582_006_volume_map.mrc as #2, grid size 456,456,456,
pixel 0.909, shown at level 0.103, step 2, values float32  
Opened cryosparc_P23_J2372_006_volume_map.mrc as #3, grid size 456,456,456,
pixel 0.909, shown at level 0.139, step 2, values float32  
Opened Productive_Ser_5mM_Ca_HoloM1_J1524_map_1.mrc as #6, grid size
384,384,384, pixel 0.999, shown at level 0.0712, step 2, values float32  

> view name session-start

opened ChimeraX session  

> show #!7 models

> select #1/A

8068 atoms, 9036 bonds, 375 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #5#!7 to #1 & sel

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 Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb, chain A (#5), sequence alignment score
= 1496  
RMSD between 156 pruned atom pairs is 1.086 angstroms; (across all 374 pairs:
3.812)  

Matchmaker Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb, chain A (#7),
sequence alignment score = 1491.1  
RMSD between 208 pruned atom pairs is 0.979 angstroms; (across all 374 pairs:
3.576)  


> matchmaker #5#!7 to #1 & sel

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 Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb, chain A (#5), sequence alignment score
= 1496  
RMSD between 156 pruned atom pairs is 1.086 angstroms; (across all 374 pairs:
3.812)  

Matchmaker Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb, chain A (#1) with
Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb, chain A (#7),
sequence alignment score = 1491.1  
RMSD between 208 pruned atom pairs is 0.979 angstroms; (across all 374 pairs:
3.576)  


> select clear

Drag select of 394 atoms, 698 residues, 412 bonds  

> hide sel atoms

> select clear

Drag select of 238 atoms, 708 residues, 250 bonds  

> hide sel atoms

> select clear

> hide #!7 models

Drag select of 120 atoms, 200 residues, 125 bonds  

> hide sel atoms

> select clear

> select add #1/C:0

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #1/C:-1

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #1/C:-2

62 atoms, 66 bonds, 3 residues, 1 model selected  

> hide sel atoms

> select add #1/A:333

84 atoms, 90 bonds, 4 residues, 1 model selected  

> select add #1/C:76

104 atoms, 111 bonds, 5 residues, 1 model selected  

> select add #1/C:75

124 atoms, 132 bonds, 6 residues, 1 model selected  

> hide sel atoms

> select add #1/A:254

146 atoms, 156 bonds, 7 residues, 1 model selected  

> hide sel atoms

> select add #1/A:332

169 atoms, 181 bonds, 8 residues, 1 model selected  

> hide sel atoms

Drag select of 31 atoms, 150 residues, 28 bonds  

> ~label sel residues

> select clear

> select add #1/C:-1

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

> select add #1/C:-2

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #1/C:0

62 atoms, 66 bonds, 3 residues, 1 model selected  

> select add #1/C:75

82 atoms, 87 bonds, 4 residues, 1 model selected  

> select add #1/A:295

104 atoms, 111 bonds, 5 residues, 1 model selected  

> select add #1/C:76

124 atoms, 132 bonds, 6 residues, 1 model selected  

> select add #1/A:296

147 atoms, 157 bonds, 7 residues, 1 model selected  

> select add #1/A:332

170 atoms, 182 bonds, 8 residues, 1 model selected  

> ~label sel residues

> select add #1/C:77

193 atoms, 207 bonds, 9 residues, 1 model selected  

> select clear

> select #1/C:77

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/C:76

43 atoms, 46 bonds, 2 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> show sel atoms

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> select clear

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 23 atom styles  

> select clear

> select add #1/A:68

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #1/A:67

45 atoms, 49 bonds, 2 residues, 1 model selected  

> select add #1/A:69

65 atoms, 70 bonds, 3 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> select add #1/C:77@O3'

66 atoms, 70 bonds, 4 residues, 1 model selected  

> select up

88 atoms, 97 bonds, 4 residues, 1 model selected  

> select up

90 atoms, 99 bonds, 5 residues, 1 model selected  

> select up

108 atoms, 119 bonds, 5 residues, 1 model selected  

> select add #1/A:352

130 atoms, 143 bonds, 6 residues, 1 model selected  

> select add #1/A:351

152 atoms, 167 bonds, 7 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel atoms

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> color sel byhetero

> show (sel-residues & sidechain) target ab

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> hide sel atoms

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 152 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select Mg

26 atoms, 26 residues, 2 models selected  

> show (#!1 & sel) target ab

> select clear

> select add #1/D:14@MG

1 atom, 1 residue, 1 model selected  

> select add #1/C:77@OP2

2 atoms, 2 residues, 1 model selected  

> ui tool show Distances

> distance #1/D:14@MG #1/C:77@OP2

Distance between Int_2_5mM_Mg_3UAA_Ser_J2582-coot-1.pdb #1/D MG 14 MG and /C G
77 OP2: 11.76Å  

> select clear

> select #1/D:14@MG

1 atom, 1 residue, 1 model selected  

> color sel red

> color sel blue

> color sel cyan

> color sel orange

> color sel light sea green

> color sel forest green

> ui tool show "Color Actions"

> color sel magenta

> select clear

> hide #!1 models

> show #!1 models

> show #!7 models

> hide #!1 models

> hide #!4 models

> hide #4.1 models

> show #!4 models

> show #4.1 models

> select add #7/A:248

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select clear

> select add #7/A:248

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #7/A:254

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select add #7/A:295

66 atoms, 72 bonds, 3 residues, 1 model selected  

> select add #7/C:76

86 atoms, 93 bonds, 4 residues, 1 model selected  
Drag select of 2 atoms, 5 residues, 2 bonds  

> select clear

Drag select of 115 atoms, 198 residues, 122 bonds  

> hide sel atoms

> ~label sel residues

> select #7/A:339

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

> select clear

> select add #7/A:248

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #7/C:165

44 atoms, 48 bonds, 2 residues, 1 model selected  

> select add #7/C:166

66 atoms, 72 bonds, 3 residues, 1 model selected  

> select add #7/A:253

86 atoms, 93 bonds, 4 residues, 1 model selected  

> select subtract #7/A:253

66 atoms, 72 bonds, 3 residues, 1 model selected  

> select add #7/A:333

88 atoms, 96 bonds, 4 residues, 1 model selected  

> select add #7/A:332

111 atoms, 121 bonds, 5 residues, 1 model selected  

> hide sel atoms

> select add #7/B:17

122 atoms, 132 bonds, 6 residues, 1 model selected  

> select add #7/B:86

133 atoms, 142 bonds, 7 residues, 1 model selected  

> select add #7/B:26

144 atoms, 152 bonds, 8 residues, 1 model selected  

> select add #7/B:25

152 atoms, 159 bonds, 9 residues, 1 model selected  

> select add #7/B:13

163 atoms, 170 bonds, 10 residues, 1 model selected  

> hide sel atoms

> select clear

> show #!1 models

> hide #!1 models

> select clear

> select Mg

26 atoms, 26 residues, 2 models selected  

> show (#!7 & sel) target ab

> select clear

> select #7/D:14@MG

1 atom, 1 residue, 1 model selected  

> color sel magenta

> select clear

> select add #7/C:76

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

> select add #7/C:77

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #7/A:68

66 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #7/A:67

88 atoms, 95 bonds, 4 residues, 1 model selected  

> select add #7/A:69

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select add #7/A:352

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select add #7/A:351

152 atoms, 164 bonds, 7 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> show #!1 models

> hide #!1 models

> color sel byhetero

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> transparency #7/a 80 rings

> transparency #7/a 0 rings

> transparency #7/b 0 rings

> transparency #7/c 0 rings

> show #!1 models

> hide #!1 models

> label sel text "{0.name} {0.number}{0.insertion_code}"

> show #!1 models

> hide #!1 models

> show #5 models

> hide #!7 models

> select add #7

12689 atoms, 14097 bonds, 670 residues, 2 models selected  

> transparency #7/c 80 ribbons

> transparency #5/c 80 ribbons

> transparency #5/a 80 ribbons

> transparency #5/b 80 ribbons

> hide #5 atoms

> select clear

> select Ca

5 atoms, 5 residues, 1 model selected  

> show sel target ab

> select clear

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:68

24 atoms, 25 bonds, 2 residues, 1 model selected  

> select add #5/A:67

46 atoms, 49 bonds, 3 residues, 1 model selected  

> select add #5/A:69

66 atoms, 70 bonds, 4 residues, 1 model selected  

> select add #5/C:77

89 atoms, 95 bonds, 5 residues, 1 model selected  

> select add #5/C:76

109 atoms, 116 bonds, 6 residues, 1 model selected  

> select add #5/A:351

131 atoms, 140 bonds, 7 residues, 1 model selected  

> select add #5/A:352

153 atoms, 164 bonds, 8 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> ~label sel residues

> select clear

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> color sel magenta

> select clear

> show #!1 models

> show #!7 models

> hide #!1 models

> hide #!5 models

> hide #!7 models

> show #!5 models

> select clear

> select #5/C:77@OP1

1 atom, 1 residue, 1 model selected  

> select up

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #5/C:76@O3'

24 atoms, 25 bonds, 2 residues, 1 model selected  

> select up

43 atoms, 47 bonds, 2 residues, 1 model selected  

> select add #5/A:67@P

44 atoms, 47 bonds, 3 residues, 1 model selected  

> select up

65 atoms, 71 bonds, 3 residues, 1 model selected  

> select add #5/A:68@OP1

66 atoms, 71 bonds, 4 residues, 1 model selected  

> select up

88 atoms, 97 bonds, 4 residues, 1 model selected  

> select add #5/A:351@O3'

89 atoms, 97 bonds, 5 residues, 1 model selected  

> select up

110 atoms, 121 bonds, 5 residues, 1 model selected  

> select add #5/A:352@C4'

111 atoms, 122 bonds, 6 residues, 1 model selected  

> select subtract #5/A:352@C4'

110 atoms, 121 bonds, 5 residues, 1 model selected  

> select add #5/A:352@C4'

111 atoms, 121 bonds, 6 residues, 1 model selected  

> select up

132 atoms, 146 bonds, 6 residues, 1 model selected  

> select add #5/A:69@O5'

133 atoms, 146 bonds, 7 residues, 1 model selected  

> select up

152 atoms, 168 bonds, 7 residues, 1 model selected  

> hide (sel-residues & (protein|nucleic)) target a

> cartoon hide sel-residues

> show (sel-residues & backbone) target ab

> color sel byhetero

> select clear

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/C:77@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/C:77@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /C G
77 OP1: 2.14Å  

> select clear

> show #!1 models

> show #!7 models

> hide #!5 models

> hide #!1 models

> select add #7/C:77@OP1

1 atom, 1 residue, 1 model selected  

> select add #7/D:14@MG

2 atoms, 2 residues, 1 model selected  

> distance #7/C:77@OP1 #7/D:14@MG

Distance between Int_1_5mM_Mg_UAA_J2372_1-coot-1_real_space_refined_001.pdb
#7/C G 77 OP1 and /D MG 14 MG: 10.79Å  

> show #!1 models

> show #!5 models

> hide #!1 models

> hide #!7 models

> hide #!5 models

> show #!1 models

> show #!7 models

> hide #!4 models

> show #!4 models

> hide #!1 models

> show #!1 models

> show #!5 models

> hide #!1 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!7 models

> show #!1 models

> hide #!5 models

> hide #!1 models

> show #!5 models

> hide #!5 models

> show #!5 models

> show #!6 models

> hide #!6 models

> show #!7 models

> hide #!5 models

> show #!1 models

> hide #!1 models

> save /Users/bhogeba/Desktop/image4.png supersample 3

> hide #!7 models

> show #!1 models

> show #!5 models

> hide #!1 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!5 models

> hide #!7 models

> show #!5 models

> save /Users/bhogeba/Desktop/image5.png supersample 3

> show #!1 models

> hide #!5 models

> save /Users/bhogeba/Desktop/image6.png supersample 3

> hide #!1 models

> show #!6 models

> show #!7 models

> hide #!6 models

> save /Users/bhogeba/Desktop/image7.png supersample 3

> show #!5 models

> hide #!7 models

> select add #7

12689 atoms, 14097 bonds, 1 pseudobond, 670 residues, 3 models selected  

> select subtract #7

Nothing selected  

> select #5/C:161

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

> select add #5/C:162

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #5/C:163

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add #5/C:164

83 atoms, 88 bonds, 4 residues, 1 model selected  

> select add #5/C:165

105 atoms, 112 bonds, 5 residues, 1 model selected  

> select subtract #5/C:161

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select subtract #5/C:162

65 atoms, 70 bonds, 3 residues, 1 model selected  

> show sel atoms

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 65 atom styles  

> select add #5/A:294

85 atoms, 91 bonds, 4 residues, 1 model selected  

> select add #5/A:295

107 atoms, 115 bonds, 5 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 107 atom styles  

> select add #5/A:293

130 atoms, 140 bonds, 6 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 130 atom styles  

> select #5/A:50

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

> select clear

> select #5/A:296

23 atoms, 25 bonds, 1 residue, 1 model selected  

> select add #5/A:297

46 atoms, 50 bonds, 2 residues, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 46 atom styles  

> hide sel atoms

> select clear

> select #5/A:295

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select add #5/A:294

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select add #5/A:293

65 atoms, 70 bonds, 3 residues, 1 model selected  

> select add #5/C:165

87 atoms, 94 bonds, 4 residues, 1 model selected  

> select add #5/C:164

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add #5/C:163

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select subtract #5/C:164

110 atoms, 119 bonds, 5 residues, 1 model selected  

> select add #5/C:164

130 atoms, 140 bonds, 6 residues, 1 model selected  

> select subtract #5/C:163

107 atoms, 115 bonds, 5 residues, 1 model selected  

> select add #5/C:163

130 atoms, 140 bonds, 6 residues, 1 model selected  

> color sel byhetero

> select clear

> select add #5/C:164

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

> select add #5/C:165

42 atoms, 45 bonds, 2 residues, 1 model selected  

> select subtract #5/C:165

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

> select add #5/A:293

43 atoms, 46 bonds, 2 residues, 1 model selected  

> select add #5/A:294

63 atoms, 67 bonds, 3 residues, 1 model selected  

> select add #5/A:295

85 atoms, 91 bonds, 4 residues, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select add #5/C:163

108 atoms, 116 bonds, 5 residues, 1 model selected  

> select add #5/C:165

130 atoms, 140 bonds, 6 residues, 1 model selected  

> label sel text "{0.name} {0.number}{0.insertion_code}"

> select #5/C:164@O2

1 atom, 1 residue, 1 model selected  

> select add #5/A:295@N6

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

0 hydrogen bonds found  

> select clear

> select add #5/C:164@O4

1 atom, 1 residue, 1 model selected  

> select add #5/A:295@N6

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

0 hydrogen bonds found  

> select clear

> select #5/C:164@O2

1 atom, 1 residue, 1 model selected  

> select add #5/A:294@O2

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

0 hydrogen bonds found  

> select #5/A:295@N1

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> select clear

> select add #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@O2

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> select clear

> select add #5/C:165@O4'

1 atom, 1 residue, 1 model selected  

> select add #5/A:293@O6

2 atoms, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> hbonds sel dashes 6 select true reveal true retainCurrent true

1 hydrogen bonds found  

> select #5/A:295

22 atoms, 24 bonds, 1 residue, 1 model selected  

> select #5/A:294

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

> save /Users/bhogeba/Desktop/image8.png supersample 3

> select clear

> select #5/A:294

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

> select add #5/C:164

40 atoms, 42 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel dashes 6 select true reveal true retainCurrent true

8 hydrogen bonds found  

> hbonds sel dashes 6 select true reveal true retainCurrent true

15 hydrogen bonds found  

> select clear

> select #5/A:295

22 atoms, 24 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> select clear

> select add #5/A:294@O2'

1 atom, 1 pseudobond, 1 residue, 2 models selected  

> select add #5/A:295

23 atoms, 24 bonds, 1 pseudobond, 2 residues, 2 models selected  

> hbonds delete

> select clear

> select #5/C:164@N3

1 atom, 1 residue, 1 model selected  

> select add #5/A:294@O2

2 atoms, 2 residues, 1 model selected  

> hbonds select

Missing "select" keyword's argument  

> ui tool show H-Bonds

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select #5/A:294@O2

1 atom, 1 residue, 1 model selected  

> select #5/A:294@N3

1 atom, 1 residue, 1 model selected  

> select #5/A:294

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

> select #5/C:164@N3

1 atom, 1 residue, 1 model selected  

> select add #5/A:294@O2

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select add #5/C:164@N3

1 atom, 1 residue, 1 model selected  

> select #5/C:164@O4

1 atom, 1 residue, 1 model selected  

> select add #5/A:295@N1

2 atoms, 2 residues, 1 model selected  

> select clear

> select #5/A:295@N1

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

1 hydrogen bonds found  

> select clear

> select #5/C:163@O2'

1 atom, 1 residue, 1 model selected  

> select clear

> select #5/C:164@O2'

1 atom, 1 residue, 1 model selected  

> select add #5/A:293@N2

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

0 hydrogen bonds found  

> select #5/A:295@N1

1 atom, 1 residue, 1 model selected  

> select add #5/C:164@N3

2 atoms, 2 residues, 1 model selected  

> hbonds sel restrict both select true reveal true

1 hydrogen bonds found  

> select clear

> save /Users/bhogeba/Desktop/image9.png supersample 3

> save /Users/bhogeba/Desktop/image10.png supersample 3

> select add #5/C:0

22 atoms, 24 bonds, 1 residue, 1 model selected  

> show sel atoms

> nucleotides sel atoms

> style nucleic & sel stick

Changed 22 atom styles  

> select clear

> select #5/C:158

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

> select add #5/C:159

40 atoms, 42 bonds, 2 residues, 1 model selected  

> select add #5/C:157

63 atoms, 67 bonds, 3 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select clear

> select #5/C:0

22 atoms, 24 bonds, 1 residue, 1 model selected  

> color sel byhetero

> save /Users/bhogeba/Desktop/image11.png supersample 3

> ui tool show "Model Panel"

> ui tool show "Side View"

> select clear

> select #5/F:2@CA

1 atom, 1 residue, 1 model selected  

> color sel hot pink

> color sel orange

> color sel red

> color sel orange red

> color sel orange

> color sel yellow

> color sel orange

> color sel cornflower blue

> color sel light sea green

> color sel dodger blue

> color sel blue

> color sel pale violet red

> color sel deep pink

> color sel magenta

> color sel rebecca purple

> color sel dark slate blue

> color sel slate blue

> color sel medium slate blue

> color sel dim gray

> color sel pale green

> color sel light green

> color sel burly wood

> color sel light coral

> color sel burly wood

> color sel tan

> color sel burly wood

> color sel aquamarine

> color sel sky blue

> color sel light sky blue

> color sel light blue

> color sel light steel blue

> color sel silver

> color sel thistle

> color sel rosy brown

> ui tool show Distances

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:67@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/A:67@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
67 OP1: 1.88Å  

> select clear

> select #5/A:67@OP2

1 atom, 1 residue, 1 model selected  

> select add #5/F:2@CA

2 atoms, 2 residues, 1 model selected  

> distance #5/A:67@OP2 #5/F:2@CA

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A A 67 OP2 and /F
CA 2 CA: 2.12Å  

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:352@OP2

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/A:352@OP2

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
352 OP2: 1.95Å  

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/A:351@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/A:351@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /A A
351 OP1: 1.91Å  

> distance style symbol false

> distance style symbol true

> label size 2

> label size 1

> label size 150

> label height 1.5

> label height 1

> label height 0.5

> select #5/F:5@CA

1 atom, 1 residue, 1 model selected  

> select add #5/C:76@O3'

2 atoms, 2 residues, 1 model selected  

> distance #5/F:5@CA #5/C:76@O3'

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 5 CA and /C U
76 O3': 2.21Å  

> label height 0.5

> select #5/F:2@CA

1 atom, 1 residue, 1 model selected  

> select add #5/C:77@OP1

2 atoms, 2 residues, 1 model selected  

> distance #5/F:2@CA #5/C:77@OP1

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/F CA 2 CA and /C G
77 OP1: 2.71Å  

> label height 0.5

> select #5/A:68@OP2

1 atom, 1 residue, 1 model selected  

> select add #5/F:2@CA

2 atoms, 2 residues, 1 model selected  

> distance #5/A:68@OP2 #5/F:2@CA

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A G 68 OP2 and /F
CA 2 CA: 2.89Å  

> label height 0.5

> select add #5/F:2@CA

21 atoms, 2 residues, 1 model selected  
Exactly two atoms must be selected!  

> select clear

> nucleotides sel atoms

> style nucleic & sel stick

Changed 20 atom styles  

> show sel atoms

> select clear

> select #5/A:69@O4

1 atom, 1 residue, 1 model selected  

> select add #5/F:2@CA

2 atoms, 2 residues, 1 model selected  

> distance #5/A:69@O4 #5/F:2@CA

Distance between Final_Prod_5mM_Ca_Ser_J1524-coot-3.pdb #5/A U 69 O4 and /F CA
2 CA: 1.91Å  

> label height 0.5

> select clear

> select #5/F:2@CA

1 atom, 1 residue, 1 model selected  

> ui tool show "Selection Inspector"

> style sel ball

Changed 1 atom style  

> style sel stick

Changed 1 atom style  

> style sel ball

Changed 1 atom style  

> style sel sphere

Changed 1 atom style  

> select down

1 atom, 1 residue, 1 model selected  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.10rc202506100450 (2025-06-10)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/bhogeba/T4_dimeric tRNA/Gst_RNP/J1387_GstRNR.pdb"

Chain information for J1387_GstRNR.pdb #1  
---  
Chain | Description  
A | No description available  

Computing secondary structure  




OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

   Hardware Overview:

     Model Name: MacBook Pro
     Model Identifier: Mac15,6
     Model Number: Z1AU00299LL/A
     Chip: Apple M3 Pro
     Total Number of Cores: 11 (5 Performance and 6 Efficiency)
     Memory: 18 GB
     System Firmware Version: 13822.81.10
     OS Loader Version: 13822.81.10

Software:

   System Software Overview:

     System Version: macOS 26.3.1 (25D2128)
     Kernel Version: Darwin 25.3.0
     Time since boot: 9 days, 19 hours, 58 minutes

Graphics/Displays:

   Apple M3 Pro:

     Chipset Model: Apple M3 Pro
     Type: GPU
     Bus: Built-In
     Total Number of Cores: 14
     Vendor: Apple (0x106b)
     Metal Support: Metal 4
     Displays:
       Color LCD:
         Display Type: Built-in Liquid Retina XDR Display
         Resolution: 3024 x 1964 Retina
         Main Display: Yes
         Mirror: Off
         Online: Yes
         Automatically Adjust Brightness: Yes
         Connection Type: Internal
       DELL P2715Q:
         Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
         UI Looks like: 1920 x 1080 @ 30.00Hz
         Mirror: Off
         Online: Yes
         Rotation: Supported
       DELL P2715Q:
         Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
         UI Looks like: 1920 x 1080 @ 60.00Hz
         Mirror: Off
         Online: Yes
         Rotation: Supported


Installed Packages:
   alabaster: 1.0.0
   appdirs: 1.4.4
   appnope: 0.1.4
   asttokens: 3.0.0
   auditwheel: 6.4.0
   babel: 2.17.0
   beautifulsoup4: 4.13.3
   blockdiag: 3.0.0
   blosc2: 3.3.4
   build: 1.2.2.post1
   certifi: 2023.11.17
   cftime: 1.6.4.post1
   charset-normalizer: 3.4.2
   ChimeraX-AddCharge: 1.5.19
   ChimeraX-AddH: 2.2.7
   ChimeraX-AlignmentAlgorithms: 2.0.2
   ChimeraX-AlignmentHdrs: 3.6.1
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.20.2
   ChimeraX-AlphaFold: 1.0.1
   ChimeraX-AltlocExplorer: 1.1.2
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Aniso: 1.1.4
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.60.7
   ChimeraX-AtomicLibrary: 14.1.18
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.4
   ChimeraX-BasicActions: 1.1.3
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 3.0.0
   ChimeraX-Boltz: 1.0
   ChimeraX-BondRot: 2.0.4
   ChimeraX-BugReporter: 1.0.2
   ChimeraX-BuildStructure: 2.13.1
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.5.1
   ChimeraX-ButtonPanel: 1.0.1
   ChimeraX-CageBuilder: 1.0.1
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.4
   ChimeraX-ChangeChains: 1.1
   ChimeraX-CheckWaters: 1.5
   ChimeraX-ChemGroup: 2.0.2
   ChimeraX-Clashes: 2.3
   ChimeraX-ColorActions: 1.0.5
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.8
   ChimeraX-CommandLine: 1.3
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.10rc202506100450
   ChimeraX-CoreFormats: 1.2
   ChimeraX-coulombic: 1.4.5
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.4
   ChimeraX-Dicom: 1.2.7
   ChimeraX-DistMonitor: 1.4.2
   ChimeraX-DockPrep: 1.1.4
   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: 1.4.1
   ChimeraX-Hbonds: 2.5.1
   ChimeraX-Help: 1.3
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.3
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-IUPAC: 1.0
   ChimeraX-KVFinder: 1.6.2
   ChimeraX-Label: 1.1.14
   ChimeraX-ListInfo: 1.2.2
   ChimeraX-Log: 1.2
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.9.1
   ChimeraX-Map: 1.3
   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: 2.2.1
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.10.1
   ChimeraX-MedicalToolbar: 1.1
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.16
   ChimeraX-MMTF: 2.2
   ChimeraX-ModelArchive: 1.0
   ChimeraX-Modeller: 1.5.19
   ChimeraX-ModelPanel: 1.5.1
   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-MutationScores: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nifti: 1.2
   ChimeraX-NMRSTAR: 1.0.2
   ChimeraX-NRRD: 1.2
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.14.1
   ChimeraX-OrthoPick: 1.0.1
   ChimeraX-PDB: 2.7.10
   ChimeraX-PDBBio: 1.0.1
   ChimeraX-PDBLibrary: 1.0.4
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0.1
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.1.3
   ChimeraX-ProfileGrids: 1.1.2
   ChimeraX-PubChem: 2.2
   ChimeraX-QScore: 1.2
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.6.3
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.3.1
   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: 2.0.3
   ChimeraX-Segger: 1.0
   ChimeraX-Segment: 1.0.1
   ChimeraX-Segmentations: 3.5.7
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.17.1
   ChimeraX-Shape: 1.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.2.1
   ChimeraX-ShowSequences: 1.0.3
   ChimeraX-SideView: 1.0.1
   ChimeraX-SimilarStructures: 1.0.1
   ChimeraX-Smiles: 2.1.2
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.19.1
   ChimeraX-STL: 1.0.1
   ChimeraX-Storm: 1.0
   ChimeraX-StructMeasure: 1.2.1
   ChimeraX-Struts: 1.0.1
   ChimeraX-Surface: 1.0.1
   ChimeraX-SwapAA: 2.0.1
   ChimeraX-SwapRes: 2.5.2
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-TaskManager: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.2.3
   ChimeraX-ToolshedUtils: 1.2.4
   ChimeraX-Topography: 1.0
   ChimeraX-ToQuest: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.45.1
   ChimeraX-Umap: 1.0
   ChimeraX-uniprot: 2.3.1
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.4.4
   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: 1.1.5
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.2.2
   contourpy: 1.3.2
   coverage: 7.8.2
   cxservices: 1.2.3
   cycler: 0.12.1
   Cython: 3.0.12
   debugpy: 1.8.14
   decorator: 5.2.1
   docutils: 0.21.2
   executing: 2.2.0
   filelock: 3.18.0
   fonttools: 4.58.2
   funcparserlib: 2.0.0a0
   glfw: 2.9.0
   grako: 3.16.5
   h5py: 3.14.0
   html2text: 2024.2.26
   idna: 3.10
   ihm: 2.2
   imagecodecs: 2024.6.1
   imagesize: 1.4.1
   iniconfig: 2.1.0
   ipykernel: 6.29.5
   ipython: 8.26.0
   ipywidgets: 8.1.7
   jedi: 0.19.1
   Jinja2: 3.1.6
   jupyter_client: 8.6.3
   jupyter_core: 5.8.1
   jupyterlab_widgets: 3.0.15
   kiwisolver: 1.4.8
   line_profiler: 4.2.0
   lxml: 5.3.1
   lz4: 4.4.4
   MarkupSafe: 3.0.2
   matplotlib: 3.10.1
   matplotlib-inline: 0.1.7
   msgpack: 1.1.0
   ndindex: 1.10.0
   nest-asyncio: 1.6.0
   netCDF4: 1.6.5
   networkx: 3.3
   nibabel: 5.2.0
   nptyping: 2.5.0
   numexpr: 2.11.0
   numpy: 1.26.4
   OpenMM: 8.2.0
   openvr: 1.26.701
   packaging: 24.2
   ParmEd: 4.2.2
   parso: 0.8.4
   pep517: 0.13.1
   pexpect: 4.9.0
   pickleshare: 0.7.5
   pillow: 10.4.0
   pip: 25.0.1
   pkginfo: 1.11.1
   platformdirs: 4.3.8
   pluggy: 1.6.0
   prompt_toolkit: 3.0.51
   psutil: 7.0.0
   ptyprocess: 0.7.0
   pure_eval: 0.2.3
   py-cpuinfo: 9.0.0
   pycollada: 0.8
   pydicom: 2.4.4
   pyelftools: 0.32
   Pygments: 2.18.0
   pynmrstar: 3.3.5
   pynrrd: 1.0.0
   PyOpenGL: 3.1.9
   PyOpenGL-accelerate: 3.1.9
   pyopenxr: 1.1.4501
   pyparsing: 3.2.3
   pyproject_hooks: 1.2.0
   PyQt6-commercial: 6.8.1
   PyQt6-Qt6: 6.8.2
   PyQt6-WebEngine-commercial: 6.8.0
   PyQt6-WebEngine-Qt6: 6.8.2
   PyQt6_sip: 13.10.0
   pytest: 8.4.0
   pytest-cov: 6.1.1
   python-dateutil: 2.9.0.post0
   pytz: 2025.2
   pyzmq: 26.4.0
   qtconsole: 5.5.2
   QtPy: 2.4.3
   qtshim: 1.1
   RandomWords: 0.4.0
   requests: 2.32.3
   roman-numerals-py: 3.1.0
   scipy: 1.14.0
   setuptools: 78.1.0
   sfftk-rw: 0.8.1
   six: 1.16.0
   snowballstemmer: 3.0.1
   sortedcontainers: 2.4.0
   soupsieve: 2.7
   Sphinx: 8.2.3
   sphinx-autodoc-typehints: 3.1.0
   sphinxcontrib-applehelp: 2.0.0
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 2.0.0
   sphinxcontrib-htmlhelp: 2.1.0
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 2.0.0
   sphinxcontrib-serializinghtml: 2.0.0
   stack-data: 0.6.3
   superqt: 0.7.1
   tables: 3.10.2
   tcia_utils: 1.5.1
   tifffile: 2025.3.13
   tinyarray: 1.2.4
   tornado: 6.5.1
   traitlets: 5.14.3
   typing_extensions: 4.14.0
   tzdata: 2025.2
   urllib3: 2.4.0
   wcwidth: 0.2.13
   webcolors: 24.11.1
   wheel: 0.45.1
   wheel-filename: 1.4.2
   widgetsnbextension: 4.0.14
#20136 duplicate Crash on Mac waking from sleep Eric Pettersen taic@…
Description 
The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x000000031e473000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031d467000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031c45b000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031b44f000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031a443000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000319437000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031842b000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031741f000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000316413000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000315407000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003143fb000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003133ef000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003123e3000 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001f088a0c0 (most recent call first):
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
 File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in 
 File "", line 88 in _run_code
 File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, lxml._elementpath, lxml.etree, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast (total: 62)


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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  

You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_0.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_1.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_2.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_3.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_4.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_0.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_0.cif #6  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_1.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_1.cif #7  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_2.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_2.cif #8  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_3.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_3.cif #9  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_4.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_4.cif #10  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_0.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_0.cif #11  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_1.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_1.cif #12  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_2.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_2.cif #13  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_3.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_3.cif #14  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_4.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_4.cif #15  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  

Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #2-15 to #1

Computing secondary structure  
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 fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_1.cif, chain D (#2), sequence alignment score =
1469.5  
RMSD between 112 pruned atom pairs is 0.263 angstroms; (across all 274 pairs:
20.703)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_2.cif, chain D (#3), sequence alignment score =
1469.5  
RMSD between 158 pruned atom pairs is 0.262 angstroms; (across all 274 pairs:
18.950)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_3.cif, chain D (#4), sequence alignment score =
1460.5  
RMSD between 152 pruned atom pairs is 0.237 angstroms; (across all 274 pairs:
20.473)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_4.cif, chain D (#5), sequence alignment score =
1451.5  
RMSD between 141 pruned atom pairs is 0.178 angstroms; (across all 274 pairs:
19.690)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_0.cif, chain D (#6), sequence alignment score =
1288.3  
RMSD between 177 pruned atom pairs is 0.529 angstroms; (across all 274 pairs:
12.666)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_1.cif, chain D (#7), sequence alignment score =
1297.3  
RMSD between 176 pruned atom pairs is 0.520 angstroms; (across all 274 pairs:
10.517)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_2.cif, chain D (#8), sequence alignment score =
1295.5  
RMSD between 178 pruned atom pairs is 0.578 angstroms; (across all 274 pairs:
10.087)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_3.cif, chain D (#9), sequence alignment score =
1300.9  
RMSD between 177 pruned atom pairs is 0.531 angstroms; (across all 274 pairs:
10.467)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_4.cif, chain D (#10), sequence alignment score =
1284.7  
RMSD between 176 pruned atom pairs is 0.531 angstroms; (across all 274 pairs:
13.215)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_0.cif, chain D (#11), sequence alignment score =
1449.7  
RMSD between 179 pruned atom pairs is 0.451 angstroms; (across all 274 pairs:
7.791)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_1.cif, chain D (#12), sequence alignment score =
1453.3  
RMSD between 179 pruned atom pairs is 0.374 angstroms; (across all 274 pairs:
10.016)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_2.cif, chain D (#13), sequence alignment score =
1464.1  
RMSD between 181 pruned atom pairs is 0.296 angstroms; (across all 274 pairs:
8.969)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_3.cif, chain D (#14), sequence alignment score =
1471.3  
RMSD between 172 pruned atom pairs is 0.272 angstroms; (across all 274 pairs:
15.272)  

Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_4.cif, chain D (#15), sequence alignment score =
1458.7  
RMSD between 165 pruned atom pairs is 0.463 angstroms; (across all 274 pairs:
19.186)  


> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> color #1 bychain

> show #2 models

> show #3 models

> show #4 models

> show #5 models

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> show #2 models

> show #3 models

> show #4 models

> show #5 models

> hide #1 models

> delete atoms #2-5

> delete bonds #2-5

> show #1 models

> hide #1 models

> show #6 models

> show #7 models

> show #8 models

> show #9 models

> show #10 models

> ui tool show "Color Actions"

> set bgColor white

> hide #7 models

> hide #8 models

> show #8 models

> show #7 models

> show #6-10 surfaces

> select /C

740 atoms, 730 bonds, 99 residues, 11 models selected  

> hide sel & #!6-10 surfaces

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide sel & #!6 surfaces

> select clear

> hide #!6 surfaces

> show #!7 models

> show #!8 models

> show #!9 models

> show #!10 models

> hide #!6-10 surfaces

> select /D

24787 atoms, 25498 bonds, 3034 residues, 11 models selected  

> show sel & #!6-10 surfaces

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> show #!7 models

> hide #!6 models

> show #!8 models

> hide #!7 models

> show #!10 models

> hide #!8 models

> show #11 models

> hide #!10 models

> hide #11 models

> show #!6 models

> show #!7 models

> hide #!6 models

> show #!6 models

> show #!8 models

> show #!9 models

> show #!10 models

> hide sel & #!6-10 surfaces

> hide #!6 models

> delete atoms (#!7-10 & sel)

> delete bonds (#!7-10 & sel)

> undo

> select clear

> hide #!6 models

> undo

> hide #!6 models

> delete atoms #7-10

> delete bonds #7-10

> show #!6 models

> show #11 models

> hide #!6 models

> show #12 models

> show #13 models

> show #14 models

> show #15 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> show #11 models

> hide #15 models

> show #15 models

> hide #11 models

> show #11 models

> show #12 models

> hide #15 models

> show #13 models

> hide #12 models

> show #12 models

> hide #11 models

> show #14 models

> hide #12 models

> hide #13 models

> hide #14 models

> show #!6 models

> show #11 models

> show #12 models

> hide #!6 models

> hide #11 models

> hide #12 models

> show #11 models

> color #11 bychain

> show #15 models

> hide #11 models

> color #15 bychain

> show #!6 models

> hide #15 models

> color #!6 bychain

> show #1 models

> hide #1 models

> show #11 models

> hide #!6 models

> show #12 models

> show #13 models

> show #14 models

> show #15 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> show #!6 models

> ui tool show "Show Sequence Viewer"

> sequence chain #6/A

Alignment identifier is 6/A  

> sequence chain #6/B

Alignment identifier is 6/B  

> select
> #6/A:4-7,10-14,19-25,32-37,43-48,52-56,59-64,69-74,83-90,97-99,103-108

501 atoms, 502 bonds, 62 residues, 1 model selected  

> select #6/A:87

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #6/A:87-99

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

> ui tool show "Color Actions"

> set bgColor indian red

> set bgColor white

> color sel brown target acsp

> color sel crimson target acsp

> color sel dark red target acsp

> select #6/B:5-7,10-14,19-24,31-37,44-50,53-56,65-67,73-78,87-94,106-111

465 atoms, 466 bonds, 55 residues, 1 model selected  

> select #6/B:91

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #6/B:91-102

92 atoms, 93 bonds, 12 residues, 1 model selected  

> select #6/B:91

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #6/B:91-102

92 atoms, 93 bonds, 12 residues, 1 model selected  

> color sel maroon target acsp

> select #6/A:87

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #6/A:87-99

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

> color sel medium slate blue target acsp

> color sel indigo target acsp

> color sel medium blue target acsp

> select clear

> select /A:87-:99

Expected an objects specifier or a keyword  

> select /A:87-99

693 atoms, 700 bonds, 91 residues, 7 models selected  

> show #11 models

> show #12 models

> show #13 models

> show #14 models

> show #15 models

> show #1 models

> color sel medium blue target acsp

> select /B:91-102

644 atoms, 651 bonds, 84 residues, 7 models selected  

> color sel maroon target acsp

> hide #!6 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> show #!6 models

> hide #1 models

> show #11 models

> hide #!6 models

> show #12 models

> hide #11 models

> show #13 models

> hide #12 models

> show #14 models

> hide #13 models

> show #15 models

> hide #14 models

> show #!6 models

> hide #15 models

> show #15 models

> hide #15 models

> hide #!6 models

> show #12 models

> show #13 models

> show #14 models

> delete atoms (#12-14 & sel)

> delete bonds (#12-14 & sel)

> select clear

> undo

> show #11 models

> hide #!12 models

> hide #!13 models

> show #15 models

> hide #!14 models

> hide #15 models

> select clear

> show #!12 models

> hide #11 models

> show #!13 models

> show #!14 models

> delete atoms #12-14

> delete bonds #12-14

> show #!6 models

> show #11 models

> hide #!6 models

> show #!6 models

> hide #11 models

> show #11 models

> hide #!6 models

> show #15 models

> hide #11 models

> show #11 models

> hide #15 models

> show #15 models

> hide #11 models

> show #!6 models

> hide #15 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/TCR-
> peptide.cxs

opened ChimeraX session  

> close session

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.contacts.cxs

opened ChimeraX session  

> hide #3 models

> hide #6 models

> show #6 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #3 models

> select #6/A:5,15

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95

109 atoms, 98 bonds, 13 residues, 1 model selected  

> color sel magenta target acsp

> color sel violet target acsp

> color sel magenta target acsp

> color sel light steel blue target acsp

> color sel sky blue target acsp

> color sel cyan target acsp

> color sel magenta target acsp

> select clear

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel magenta target acsp

> select clear

> show #3,6 surfaces

> hide #!3 models

> show #!3 models

> hide #!3,6 surfaces

> show #!1 models

> hide #!1 models

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select clear

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> show sel atoms

> select clear

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> show sel surfaces

> select #6/A:73

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> select clear

> transparency #3,6 70

> transparency #3,6 40

Drag select of 1 residues  

> hide sel surfaces

> select clear

> hide #!3,6 surfaces

> show #!3,6 surfaces

> hide #!3,6 surfaces

> select #6/C:31

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel surfaces

> hide sel surfaces

> color (#!6 & sel) blue

> show sel surfaces

> select clear

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> show sel surfaces

> select clear

> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/E.coli.HqbAmutatnt_Hfq_CoA.png"
> width 900 height 668 supersample 4 transparentBackground true

> select #6/G:49@OG1

1 atom, 1 residue, 1 model selected  
Drag select of fold_hqba_hfqx6_co_model_0.cif_B SES surface, 234 of 122862
triangles  

> select #6/A:5

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #6/A:98

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #6/A:102

24 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #6/A:103

35 atoms, 32 bonds, 4 residues, 2 models selected  

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> show sel surfaces

> hide #!3 models

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> show sel surfaces

> select clear

> hide #!6 surfaces

> show #!3 models

> select #6/A:15,19,23,24,27,41,49,52,67,95,117,126,152,164,167

133 atoms, 122 bonds, 15 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pale violet red target acsp

> select clear

> select #6/A:15,19,23,24,27,41,49,52,67,95,117,126,152,164,167

133 atoms, 122 bonds, 15 residues, 1 model selected  

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> show sel surfaces

> select clear

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select clear

> select #6/A:41

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color (#!6 & sel) magenta

> select up

38 atoms, 38 bonds, 5 residues, 2 models selected  

> select up

1311 atoms, 1341 bonds, 167 residues, 2 models selected  

> show sel surfaces

> select clear

> hide #!3,6 surfaces

> undo

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> show sel surfaces

> select clear

> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/E.coli.HqbAmutatnt_Hfq_CoA.2.png"
> width 900 height 668 supersample 4 transparentBackground true

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_0.cif

Chain information for fold_hqba_yhbp_co_model_0.cif #4  
---  
Chain | Description  
A | .  
B | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif

Chain information for fold_hqba_yhbp_co_model_1.cif #5  
---  
Chain | Description  
A | .  
B | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_2.cif

Chain information for fold_hqba_yhbp_co_model_2.cif #7  
---  
Chain | Description  
A | .  
B | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_3.cif

Chain information for fold_hqba_yhbp_co_model_3.cif #8  
---  
Chain | Description  
A | .  
B | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_4.cif

Chain information for fold_hqba_yhbp_co_model_4.cif #9  
---  
Chain | Description  
A | .  
B | .  

Computing secondary structure  

> hide #4-5,7-9#!3,6 surfaces

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #4-5,7-9 to #6 & sel

Computing secondary structure  
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_0.cif, chain A (#4), sequence alignment score = 852.8  
RMSD between 167 pruned atom pairs is 0.391 angstroms; (across all 167 pairs:
0.391)  

Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)  

Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_2.cif, chain A (#7), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.278 angstroms; (across all 167 pairs:
0.278)  

Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_3.cif, chain A (#8), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.296 angstroms; (across all 167 pairs:
0.296)  

Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_4.cif, chain A (#9), sequence alignment score = 873.8  
RMSD between 167 pruned atom pairs is 0.297 angstroms; (across all 167 pairs:
0.297)  


> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #!6 models

> hide #5 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #!3 models

> show #!6 models

> show #7 models

> hide #!6 models

> show #5 models

> show #8 models

> show #9 models

> color #4-5,7-9 bychain

> select clear

> hide #5 models

> hide #7 models

> show #5 models

> hide #9 models

> hide #8 models

> show #8 models

> hide #5 models

> hide #4 models

> show #5 models

> show #7 models

> delete atoms #5,7-8

> delete bonds #5,7-8

> show #4 models

> show #9 models

> hide #9 models

> show #9 models

> hide #4 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif

Chain information for fold_hqba_yhbp_co_model_1.cif #5  
---  
Chain | Description  
A | .  
B | .  

Computing secondary structure  

> color #5,9 bychain

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> ui tool show Matchmaker

[deleted to fit within ticket limits]


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_3.cif

Chain information for fold_azor_monomer_fad_model_3.cif #9  
---  
Chain | Description  
A | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_4.cif

Chain information for fold_azor_monomer_fad_model_4.cif #10  
---  
Chain | Description  
A | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_0.cif

Summary of feedback from opening /Users/taic/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_0.cif  
---  
note | Fetching CCD NAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/NAD/NAD.cif  

Chain information for fold_azor_monomer_nad_model_0.cif #11  
---  
Chain | Description  
A | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_1.cif

Chain information for fold_azor_monomer_nad_model_1.cif #12  
---  
Chain | Description  
A | .  

Computing secondary structure  

> ui tool show Matchmaker

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_2.cif

Chain information for fold_azor_monomer_nad_model_2.cif #13  
---  
Chain | Description  
A | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_3.cif

Chain information for fold_azor_monomer_nad_model_3.cif #14  
---  
Chain | Description  
A | .  

Computing secondary structure  
[Repeated 1 time(s)]

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_nad/fold_azor_monomer_nad_model_4.cif

Chain information for fold_azor_monomer_nad_model_4.cif #15  
---  
Chain | Description  
A | .  

Computing secondary structure  

> matchmaker #2-12 to #1

Computing secondary structure  
[Repeated 11 time(s)]  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 fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_1.cif, chain A (#2), sequence alignment score = 1086.8  
RMSD between 208 pruned atom pairs is 0.117 angstroms; (across all 208 pairs:
0.117)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_2.cif, chain A (#3), sequence alignment score = 1086.8  
RMSD between 208 pruned atom pairs is 0.103 angstroms; (across all 208 pairs:
0.103)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_3.cif, chain A (#4), sequence alignment score = 1086.8  
RMSD between 208 pruned atom pairs is 0.129 angstroms; (across all 208 pairs:
0.129)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_model_4.cif, chain A (#5), sequence alignment score = 1086.8  
RMSD between 208 pruned atom pairs is 0.121 angstroms; (across all 208 pairs:
0.121)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_1.cif, chain A (#7), sequence alignment score =
1080.2  
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_2.cif, chain A (#8), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.447 angstroms; (across all 208 pairs:
0.447)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_3.cif, chain A (#9), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.420 angstroms; (across all 208 pairs:
0.420)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_4.cif, chain A (#10), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.291 angstroms; (across all 208 pairs:
0.291)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_1.cif, chain A (#12), sequence alignment score =
1080.2  
RMSD between 208 pruned atom pairs is 0.353 angstroms; (across all 208 pairs:
0.353)  


> matchmaker #13-15 to #1

Computing secondary structure  
[Repeated 3 time(s)]  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 fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_2.cif, chain A (#13), sequence alignment score =
1080.2  
RMSD between 208 pruned atom pairs is 0.368 angstroms; (across all 208 pairs:
0.368)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_3.cif, chain A (#14), sequence alignment score =
1080.2  
RMSD between 208 pruned atom pairs is 0.329 angstroms; (across all 208 pairs:
0.329)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_4.cif, chain A (#15), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.287 angstroms; (across all 208 pairs:
0.287)  


> select add #2

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> select add #3

3292 atoms, 3370 bonds, 416 residues, 2 models selected  

> select add #4

4938 atoms, 5055 bonds, 624 residues, 3 models selected  

> select add #5

6584 atoms, 6740 bonds, 832 residues, 4 models selected  

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> delete atoms sel

> delete bonds sel

> show #6 models

> hide #6 models

> show #6 models

> show #7 models

> hide #1 models

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> hide #6 models

> show #6 models

> hide #6 models

> show #6 models

> hide #7 models

> show #7 models

> hide #7 models

> show #7 models

> show #8 models

> show #9 models

> show #10 models

> select add #7

1699 atoms, 1743 bonds, 209 residues, 1 model selected  

> select add #8

3398 atoms, 3486 bonds, 418 residues, 2 models selected  

> select add #9

5097 atoms, 5229 bonds, 627 residues, 3 models selected  

> select add #10

6796 atoms, 6972 bonds, 836 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> show #11 models

> hide #6 models

> show #12 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> show #13 models

> show #14 models

> show #15 models

> select add #12

1690 atoms, 1733 bonds, 209 residues, 1 model selected  

> select add #13

3380 atoms, 3466 bonds, 418 residues, 2 models selected  

> select add #14

5070 atoms, 5199 bonds, 627 residues, 3 models selected  

> select add #15

6760 atoms, 6932 bonds, 836 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> show #1 models

> show #6 models

> hide #6 models

> hide #11 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_0.cif

Chain information for fold_azor_dimer_model_0.cif #2  
---  
Chain | Description  
A B | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_1.cif

Chain information for fold_azor_dimer_model_1.cif #3  
---  
Chain | Description  
A B | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_2.cif

Chain information for fold_azor_dimer_model_2.cif #4  
---  
Chain | Description  
A B | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_3.cif

Chain information for fold_azor_dimer_model_3.cif #5  
---  
Chain | Description  
A B | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer/fold_azor_dimer_model_4.cif

Chain information for fold_azor_dimer_model_4.cif #7  
---  
Chain | Description  
A B | .  

Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #2-7,11 to #1

Computing secondary structure  
[Repeated 7 time(s)]  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 fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2  
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_1.cif, chain A (#3), sequence alignment score = 1080.8  
RMSD between 208 pruned atom pairs is 0.383 angstroms; (across all 208 pairs:
0.383)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_2.cif, chain A (#4), sequence alignment score = 1074.2  
RMSD between 208 pruned atom pairs is 0.452 angstroms; (across all 208 pairs:
0.452)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_3.cif, chain A (#5), sequence alignment score = 1074.2  
RMSD between 208 pruned atom pairs is 0.377 angstroms; (across all 208 pairs:
0.377)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_4.cif, chain A (#7), sequence alignment score = 1077.8  
RMSD between 208 pruned atom pairs is 0.371 angstroms; (across all 208 pairs:
0.371)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)  


> show #6 models

> hide #2 models

> show #2 models

> hide #7 models

> hide #6 models

> show #7 models

> select add #3

3292 atoms, 3370 bonds, 416 residues, 1 model selected  

> select add #4

6584 atoms, 6740 bonds, 832 residues, 2 models selected  

> select add #5

9876 atoms, 10110 bonds, 1248 residues, 3 models selected  

> select add #7

13168 atoms, 13480 bonds, 1664 residues, 4 models selected  

> delete atoms sel

> delete bonds sel

> hide #1 models

> show #6 models

> hide #2 models

> select /A

6584 atoms, 6740 bonds, 832 residues, 4 models selected  

> show sel & #6 surfaces

> show #2 models

> select /B

1743 atoms, 1791 bonds, 210 residues, 3 models selected  

> hide #2 models

> show #2 models

> select #2/B

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> show sel surfaces

> hide #!6 models

> show #1 models

> show #!6 models

> hide #1 models

> hide #!6 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_0.cif

Chain information for fold_azor_dimer_fad_model_0.cif #3  
---  
Chain | Description  
A B | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_1.cif

Chain information for fold_azor_dimer_fad_model_1.cif #4  
---  
Chain | Description  
A B | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_2.cif

Chain information for fold_azor_dimer_fad_model_2.cif #5  
---  
Chain | Description  
A B | .  

Computing secondary structure  

> hide sel surfaces

> ui tool show Matchmaker

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_3.cif

Chain information for fold_azor_dimer_fad_model_3.cif #7  
---  
Chain | Description  
A B | .  


> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_fad/fold_azor_dimer_fad_model_4.cif

Chain information for fold_azor_dimer_fad_model_4.cif #8  
---  
Chain | Description  
A B | .  

Computing secondary structure  
[Repeated 1 time(s)]

> matchmaker #3-5,7-8#!6 to #1

Computing secondary structure  
[Repeated 6 time(s)]  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 fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_1.cif, chain A (#4), sequence alignment score = 1049  
RMSD between 208 pruned atom pairs is 0.456 angstroms; (across all 208 pairs:
0.456)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_2.cif, chain A (#5), sequence alignment score =
1083.2  
RMSD between 208 pruned atom pairs is 0.435 angstroms; (across all 208 pairs:
0.435)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_3.cif, chain A (#7), sequence alignment score =
1083.2  
RMSD between 208 pruned atom pairs is 0.408 angstroms; (across all 208 pairs:
0.408)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_4.cif, chain A (#8), sequence alignment score =
1083.2  
RMSD between 208 pruned atom pairs is 0.428 angstroms; (across all 208 pairs:
0.428)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)  


> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs

\u2014\u2014\u2014 End of log from Wed Feb 18 08:19:31 2026 \u2014\u2014\u2014

opened ChimeraX session  

> hide #!2 models

> hide #4 models

> hide #5 models

> hide #7 models

> hide #8 models

> show #4 models

> hide #3 models

> show #5 models

> show #7 models

> show #8 models

> select add #4

4991 atoms, 5113 bonds, 625 residues, 2 models selected  

> select add #5

8336 atoms, 8541 bonds, 1042 residues, 3 models selected  

> select add #7

11681 atoms, 11969 bonds, 1459 residues, 4 models selected  

> select add #8

15026 atoms, 15397 bonds, 1876 residues, 5 models selected  

> delete atoms (#4-5,7-8 & sel)

> delete bonds (#4-5,7-8 & sel)

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_monomer_fad/fold_azor_monomer_fad_model_0.cif

Chain information for fold_azor_monomer_fad_model_0.cif #4  
---  
Chain | Description  
A | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_AlphaFold-
> Predictions/azor_dimer_nad/fold_azor_dimer_nad_model_0.cif

Chain information for fold_azor_dimer_nad_model_0.cif #5  
---  
Chain | Description  
A B | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/icd/fold_icd_model_0.cif

Chain information for fold_icd_model_0.cif #7  
---  
Chain | Description  
A | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/mqo/fold_mqo_model_0.cif

Chain information for fold_mqo_model_0.cif #8  
---  
Chain | Description  
A | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/ndhc/fold_ndhc_model_0.cif

Chain information for fold_ndhc_model_0.cif #9  
---  
Chain | Description  
A | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/ndhf/fold_ndhf_model_0.cif

Chain information for fold_ndhf_model_0.cif #10  
---  
Chain | Description  
A | .  

Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AlphaFold-
> OtherProteins/suca/fold_suca_model_0.cif

Chain information for fold_suca_model_0.cif #12  
---  
Chain | Description  
A | .  

Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #3-5,7-12#!2,6 to #1/A pairing bs

Computing secondary structure  
[Repeated 6 time(s)]  Parameters  
---  
Chain pairing | bs  
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 fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_nad_model_0.cif, chain B (#5), sequence alignment score =
1086.8  
RMSD between 208 pruned atom pairs is 0.362 angstroms; (across all 208 pairs:
0.362)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4  
RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
21.278)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8  
RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
22.621)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2  
RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
31.595)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4  
RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
25.278)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2  
RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
17.409)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2  
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)  


> hide #12 models

> hide #10 models

> hide #9 models

> hide #8 models

> hide #7 models

> show #1 models

> hide #1 models

> show #!2 models

> hide #!2 models

> show #3 models

> hide #3 models

> hide #5 models

> show #1 models

> show #!2 models

> hide #1 models

> show #1 models

> hide #4 models

> show #3 models

> hide #!2 models

> hide #1 models

> show #!6 models

> hide #3#!6 surfaces

> show #7 models

> hide #!6 models

> hide #3 models

> show #8 models

> hide #7 models

> show #9 models

> hide #8 models

> rainbow #9

> show #10 models

> hide #9 models

> show #11 models

> hide #10 models

> show #1 models

> hide #1 models

> show #1 models

> hide #11 models

> show #11 models

> show #12 models

> hide #11 models

> hide #1 models

> matchmaker #8-10,12 to #7/A pairing bs

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bs  
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 fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56  
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)  

Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5  
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)  

Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2  
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)  

Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_suca_model_0.cif,
chain A (#12), sequence alignment score = 124  
RMSD between 16 pruned atom pairs is 1.040 angstroms; (across all 346 pairs:
29.841)  


> show #7 models

> hide #12 models

> show #8 models

> show #9 models

> hide #8 models

> hide #7 models

> show #8 models

> hide #9 models

> show #12 models

> hide #8 models

> rainbow #12

> show #7 models

> hide #12 models

> show #8 models

> hide #7 models

> show #5 models

> hide #8 models

> color #5 bychain

> show #!6 models

> hide #5 models

> show #11 models

> hide #!6 models

> show #!2 models

> hide #!2 models

> show #5 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #5 models

> select /A

32114 atoms, 32801 bonds, 4077 residues, 12 models selected  

> ui tool show Matchmaker

> matchmaker #3-5,7-12#!2,6 & sel to #1/A & sel pairing bs

Computing secondary structure  
[Repeated 6 time(s)]  Parameters  
---  
Chain pairing | bs  
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 fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2  
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1083.2  
RMSD between 208 pruned atom pairs is 0.359 angstroms; (across all 208 pairs:
0.359)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4  
RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
21.278)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8  
RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
22.621)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2  
RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
31.595)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4  
RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
25.278)  

Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2  
RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
17.409)  


> show #1 models

> hide #1 models

> show #5 models

> hide #11 models

> show #11 models

> hide #5 models

> select ::name="NAD"

88 atoms, 96 bonds, 2 residues, 2 models selected  

> select ~sel & ##selected

4938 atoms, 5055 bonds, 624 residues, 2 models selected  

> rainbow sel & #11

> select clear

> show #1 models

> hide #11 models

> open 9H2I fromDatabase pdb format mmcif

Summary of feedback from opening 9H2I fetched from pdb  
---  
note | Fetching compressed mmCIF 9h2i from http://files.rcsb.org/download/9h2i.cif  

9h2i title:  
Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of
Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate
dehydrogenase complex [more info...]  

Chain information for 9h2i #13  
---  
Chain | Description | UniProt  
A | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex | ODP2_ECOLI 314-379  
B C | Dihydrolipoyl dehydrogenase | DLDH_ECOLI 2-474  

Non-standard residues in 9h2i #13  
---  
FAD \u2014 flavin-adenine dinucleotide  


> ui tool show Matchmaker

> matchmaker #13 to #1/A pairing bs

Computing secondary structure  
Parameters  
---  
Chain pairing | bs  
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 fold_azor_monomer_model_0.cif, chain A (#1) with 9h2i, chain B
(#13), sequence alignment score = 64.3  
RMSD between 6 pruned atom pairs is 0.906 angstroms; (across all 61 pairs:
18.939)  


> undo

> select ::name="NAD"

88 atoms, 96 bonds, 2 residues, 2 models selected  

> hide #11 models

> hide #1 models

> show #4 models

> hide #13 models

> select ::name="FAD"

265 atoms, 290 bonds, 5 residues, 4 models selected  

> show #13 models

> hide #4 models

> color sel & #13 bychain

> undo

> select clear

> color #13 bychain

> undo

> select ::name="FAD"

265 atoms, 290 bonds, 5 residues, 4 models selected  

> matchmaker #13 & sel to #4/A & sel pairing bs

No 'to' chains specified  

> matchmaker #13 & sel to #4/A & sel pairing bs

No 'to' chains specified  

> matchmaker #13 & sel to #6 & sel

No matrix compatible with both reference structure and all match structures  

> select clear

> select ::name="FAD"

265 atoms, 290 bonds, 5 residues, 4 models selected  

> matchmaker #13 to #6 & sel

No matrix compatible with both reference structure and all match structures  

> matchmaker #13 to #6

Computing secondary structure  
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 fold_azor_monomer_fad_model_0.cif, chain A (#6) with 9h2i, chain B
(#13), sequence alignment score = 64.3  
RMSD between 6 pruned atom pairs is 0.976 angstroms; (across all 61 pairs:
18.887)  


> show #!6 models

> hide #13 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> open 8RX4 fromDatabase pdb format mmcif

Summary of feedback from opening 8RX4 fetched from pdb  
---  
notes | Fetching compressed mmCIF 8rx4 from http://files.rcsb.org/download/8rx4.cif  
Fetching CCD NAP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif  

8rx4 title:  
Mycothione reductase from Mycobacterium xenopi in complex with co-factor FAD
and redox co-factor NADP(H) [more info...]  

Chain information for 8rx4 #14  
---  
Chain | Description | UniProt  
A B | Mycothione reductase | X8E6Y0_MYCXE 1-459  

Non-standard residues in 8rx4 #14  
---  
FAD \u2014 flavin-adenine dinucleotide  
NAP \u2014 nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  


> hide #!6 models

> matchmaker #14 to #13

Computing secondary structure  
[Repeated 1 time(s)]  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 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3  
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)  


> show #13 models

> select ::name="FAD"

371 atoms, 406 bonds, 7 residues, 5 models selected  

> select ~sel & ##selected

21835 atoms, 21626 bonds, 3388 residues, 5 models selected  

> color sel & #13-14 bychain

> select clear

> hide #14 models

> show #14 models

> hide #13 models

> show #13 models

> hide #14 models

> show #14 models

> hide #13 models

> select #14/B

3646 atoms, 3705 bonds, 481 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #13 models

> hide #14 models

> select #13/C

3803 atoms, 3650 bonds, 693 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> hide sel atoms

> select #13/B

3924 atoms, 3668 bonds, 798 residues, 1 model selected  

> rainbow sel

> select clear

> show #4 models

> hide #13 models

> show #14 models

> show #13 models

> hide #14 models

> hide #4 models

> show #!6 models

> hide #13 models

> show #13 models

> select #13/B:429

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #13/B:429

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "move picked models"

> view matrix models
> #13,-0.24553,0.95614,-0.15973,-12.311,-0.87052,-0.14498,0.4703,-33.244,0.42651,0.25452,0.86793,37.123

> select clear

> show #3 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select ::name="FAD"

371 atoms, 406 bonds, 7 residues, 5 models selected  

> hide #13 models

> select ~sel & ##selected

21835 atoms, 21626 bonds, 3388 residues, 5 models selected  

> color sel & #3 bychain

> select clear

> show #13 models

> select #13/B:118

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.033187,-0.97762,-0.20777,14.167,0.99779,0.020425,0.063272,41.991,-0.057612,-0.20941,0.97613,20.908

> view matrix models
> #13,0.61108,-0.5049,-0.60964,43.097,0.74854,0.11812,0.65248,13.491,-0.25743,-0.85506,0.45012,36.524

Drag select of 1 residues  

> view matrix models
> #13,0.69637,-0.51088,-0.50406,42.577,0.69997,0.32838,0.6342,10.762,-0.15848,-0.79446,0.58627,34.933

> view matrix models
> #13,0.60362,-0.77451,-0.18916,31.241,0.57555,0.25913,0.77562,2.4774,-0.55171,-0.57705,0.60219,19.363

> view matrix models
> #13,0.57452,-0.7742,-0.2656,32.755,0.56401,0.13931,0.81393,1.7918,-0.59314,-0.61742,0.5167,21.081

> view matrix models
> #13,0.50768,-0.80838,-0.29797,31.826,0.63814,0.12046,0.76044,6.2021,-0.57883,-0.57621,0.57701,19.262

> view matrix models
> #13,0.41134,-0.8476,-0.33522,30.098,0.72496,0.081317,0.68397,11.956,-0.55248,-0.52437,0.64793,17.418

> view matrix models
> #13,0.50347,-0.56782,-0.65123,41.319,0.83944,0.14298,0.52431,20.563,-0.2046,-0.81064,0.54863,34.733

> view matrix models
> #13,0.81357,-0.39993,-0.42208,42.973,0.56489,0.37157,0.73677,2.4881,-0.13783,-0.83785,0.52822,37.879

> select clear

> select #13/B:81

7 atoms, 6 bonds, 1 residue, 1 model selected  

> view matrix models
> #13,0.81385,-0.37394,-0.44476,43.517,0.57225,0.38291,0.7252,3.0254,-0.10088,-0.84472,0.52562,39.27

> view matrix models
> #13,0.80931,-0.3118,-0.49779,44.601,0.58724,0.41087,0.69738,4.2194,-0.01291,-0.85672,0.51563,42.67

> view matrix models
> #13,0.83554,-0.52523,-0.16124,36.183,0.53716,0.84258,0.038938,20.618,0.11541,-0.11915,0.98615,25.714

> view matrix models
> #13,0.85682,-0.51537,0.016019,31.023,0.50956,0.85108,0.12652,16.749,-0.07884,-0.10025,0.99183,18.802

> view matrix models
> #13,0.13465,-0.7299,-0.67016,30.752,0.80312,-0.31576,0.50527,23.627,-0.58041,-0.60625,0.54368,20.54

> select clear

[Repeated 1 time(s)]Drag select of 5 residues, 1 bonds  

> show #5 models

> hide #3 models

> show #3 models

> hide #5 models

> show #14 models

> matchmaker #14 to #13

Computing secondary structure  
[Repeated 1 time(s)]  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 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3  
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)  


> hide #13 models

> show #13 models

> select ::name="FAD"

371 atoms, 406 bonds, 7 residues, 5 models selected  

> select ~sel & ##selected

21835 atoms, 21626 bonds, 3388 residues, 5 models selected  

> show sel & #3,13-14 surfaces

> hide #!14 models

> hide sel & #!3,13 surfaces

> show #!14 models

> hide #!13 models

> hide sel & #!3,14 surfaces

> select clear

> hide #!3 models

> select ::name="NAD"

88 atoms, 96 bonds, 2 residues, 2 models selected  

> select ::name="NAP"

96 atoms, 104 bonds, 2 residues, 1 model selected  

> show #!13 models

> select clear

> hide #!13 models

> show #!13 models

> hide #!13 models

> select ::name="FAD"

371 atoms, 406 bonds, 7 residues, 5 models selected  

> select ~sel & ##selected

21835 atoms, 21626 bonds, 3388 residues, 5 models selected  

> rainbow sel & #!14

> select clear

> select ::name="NAP"

96 atoms, 104 bonds, 2 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(NAP) ``  
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`  
(NAP) ``  
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`  
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAP) ``  
(NAP) ``  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAP) `Info: Total number of electrons: 384; net charge: -3`  
(NAP) ``  
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(NAP) ``  
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`  
(NAP) ``  
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`  
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAP) ``  
(NAP) ``  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAP) `Info: Total number of electrons: 384; net charge: -3`  
(NAP) ``  
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  

Contents of sqm.out:



               --------------------------------------------------------
                                AMBER SQM VERSION 19

                                        By
                 Ross C. Walker, Michael F. Crowley, Scott Brozell,
                            Tim Giese, Andreas W. Goetz,
                           Tai-Sung Lee and David A. Case

               --------------------------------------------------------


   --------------------------------------------------------------------------------
     QM CALCULATION INFO
   --------------------------------------------------------------------------------

   | QMMM: Citation for AMBER QMMM Run:
   | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008

   QMMM: SINGLET STATE CALCULATION
   QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132

   | QMMM: *** Selected Hamiltonian *** 
   | QMMM: AM1         

   | QMMM: *** Parameter sets in use ***
   | QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
   | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
   | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
   | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
   | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)

   | QMMM: *** SCF convergence criteria ***
   | QMMM: Energy change                :  0.1D-09 kcal/mol
   | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
   | QMMM: Density matrix change        :  0.5D-06
   | QMMM: Maximum number of SCF cycles :     1000

   | QMMM: *** Diagonalization Routine Information ***
   | QMMM: Pseudo diagonalizations are allowed.
   | QMMM: Auto diagonalization routine selection is in use.
   | QMMM:
   | QMMM: Timing diagonalization routines:
   | QMMM:                              norbs =      217
   | QMMM:    diag iterations used for timing =        4
   | QMMM:
   | QMMM:              Internal diag routine = 0.051654 seconds
   | QMMM:                 Dspev diag routine = 0.044332 seconds
   | QMMM:                Dspevd diag routine = 0.032116 seconds
   | QMMM:                Dspevx diag routine = 0.153242 seconds
   | QMMM:                 Dsyev diag routine = 0.047097 seconds
   | QMMM:                Dsyevd diag routine = 0.033935 seconds
   | QMMM:                Dsyevr diag routine = 0.038554 seconds
   | QMMM:
   | QMMM:                Pseudo diag routine = 0.022789 seconds
   | QMMM:
   | QMMM: Using dspevd routine (diag_routine=3).

     QMMM: QM Region Cartesian Coordinates (*=link atom) 
     QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
     QMMM:     1        1      P       17.4620    0.4650   57.8060
     QMMM:     2        2      O       16.5620   -0.5740   58.3900
     QMMM:     3        3      O       18.0440    0.2210   56.4520
     QMMM:     4        4      O       18.6480    0.7880   58.8450
     QMMM:     5        5      C       18.2700    1.3930   60.1070
     QMMM:     6        6      C       19.4870    1.8540   60.8730
     QMMM:     7        7      O       19.0230    2.6210   62.0160
     QMMM:     8        8      C       20.3910    0.7570   61.4600
     QMMM:     9        9      O       21.7470    1.1830   61.4090
     QMMM:    10       10      C       19.8810    0.6600   62.8920
     QMMM:    11       11      O       20.8230    0.1440   63.8270
     QMMM:    12       12      C       19.6340    2.1310   63.1840
     QMMM:    13       13      N       18.7140    2.3450   64.2950
     QMMM:    14       14      C       17.4200    1.8950   64.3780
     QMMM:    15       15      N       16.8230    2.2310   65.4940
     QMMM:    16       16      C       17.7860    2.9360   66.2020
     QMMM:    17       17      C       17.7680    3.5530   67.4670
     QMMM:    18       18      N       16.7090    3.5600   68.2720
     QMMM:    19       19      N       18.9020    4.1690   67.8780
     QMMM:    20       20      C       19.9640    4.1590   67.0630
     QMMM:    21       21      N       20.0960    3.6140   65.8570
     QMMM:    22       22      C       18.9590    3.0090   65.4750
     QMMM:    23       23      O       16.6940    1.8750   57.8220
     QMMM:    24       24      P       16.8310    3.1760   56.8950
     QMMM:    25       25      O       16.1610    4.3450   57.5500
     QMMM:    26       26      O       18.2590    3.2930   56.4770
     QMMM:    27       27      O       15.9430    2.7150   55.6410
     QMMM:    28       28      C       14.5280    2.4980   55.8770
     QMMM:    29       29      C       13.9670    1.5170   54.8750
     QMMM:    30       30      O       14.0230    2.0920   53.5500
     QMMM:    31       31      C       14.6700    0.1520   54.7880
     QMMM:    32       32      O       13.7350   -0.9120   54.6620
     QMMM:    33       33      C       15.5640    0.2940   53.5490
     QMMM:    34       34      O       15.7840   -0.9330   52.8700
     QMMM:    35       35      C       14.7120    1.2110   52.6690
     QMMM:    36       36      N       15.5520    2.0170   51.7640
     QMMM:    37       37      C       15.9700    1.4830   50.5670
     QMMM:    38       38      C       16.8040    2.2160   49.7300
     QMMM:    39       39      C       17.2170    1.5960   48.4310
     QMMM:    40       40      O       16.7920    0.4660   48.1440
     QMMM:    41       41      N       18.0490    2.2680   47.6420
     QMMM:    42       42      C       17.1960    3.4950   50.0970
     QMMM:    43       43      C       16.7690    4.0240   51.3000
     QMMM:    44       44      C       15.9580    3.2770   52.1340
     QMMM:    45       45      P       20.6860   -1.4490   64.0240
     QMMM:    46       46      O       21.7060   -1.8020   65.0890
     QMMM:    47       47      O       21.0090   -2.0990   62.6800
     QMMM:    48       48      O       19.2630   -1.7280   64.4740
     QMMM:    49       49      H       17.7290    0.6600   60.7060
     QMMM:    50       50      H       17.6220    2.2480   59.9150
     QMMM:    51       51      H       20.0850    2.5010   60.2310
     QMMM:    52       52      H       20.2560   -0.1860   60.9310
     QMMM:    53       53      H       22.3250    0.4250   61.5240
     QMMM:    54       54      H       18.9490    0.0970   62.9320
     QMMM:    55       55      H       20.5770    2.6470   63.3660
     QMMM:    56       56      H       16.9410    1.3200   63.5990
     QMMM:    57       57      H       15.8540    3.1050   67.9850
     QMMM:    58       58      H       16.7600    4.0200   69.1700
     QMMM:    59       59      H       20.8400    4.6670   67.4390
     QMMM:    60       60      H       14.0000    3.4470   55.7840
     QMMM:    61       61      H       14.3870    2.1050   56.8840
     QMMM:    62       62      H       12.9200    1.3420   55.1230
     QMMM:    63       63      H       15.2870   -0.0020   55.6730
     QMMM:    64       64      H       13.8800   -1.5500   55.3640
     QMMM:    65       65      H       16.5100    0.7710   53.8050
     QMMM:    66       66      H       16.3180   -1.5120   53.4190
     QMMM:    67       67      H       13.9980    0.6220   52.0930
     QMMM:    68       68      H       15.6500    0.4930   50.2770
     QMMM:    69       69      H       18.3800    3.1810   47.9180
     QMMM:    70       70      H       18.3500    1.8650   46.7660
     QMMM:    71       71      H       17.8320    4.0750   49.4450
     QMMM:    72       72      H       17.0690    5.0210   51.5890
     QMMM:    73       73      H       15.6420    3.6860   53.0820

   --------------------------------------------------------------------------------
     RESULTS
   --------------------------------------------------------------------------------


   QMMM: ERROR!
   QMMM: Unable to achieve self consistency to the tolerances specified
   QMMM: No convergence in SCF after   1000 steps.
   QMMM: E =  -0.2168E+07 DeltaE =  -0.4757E+03 DeltaP =   0.9525E+00
   QMMM: Smallest DeltaE =   0.8289E-07 DeltaP =   0.1057E-04 Step =      3




Failure running ANTECHAMBER for residue NAP Check reply log for details  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(NAP) ``  
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`  
(NAP) ``  
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`  
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAP) ``  
(NAP) ``  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAP) `Info: Total number of electrons: 384; net charge: -3`  
(NAP) ``  
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(NAP) ``  
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`  
(NAP) ``  
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`  
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAP) ``  
(NAP) ``  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAP) `Info: Total number of electrons: 384; net charge: -3`  
(NAP) ``  
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  

Contents of sqm.out:



               --------------------------------------------------------
                                AMBER SQM VERSION 19

                                        By
                 Ross C. Walker, Michael F. Crowley, Scott Brozell,
                            Tim Giese, Andreas W. Goetz,
                           Tai-Sung Lee and David A. Case

               --------------------------------------------------------


   --------------------------------------------------------------------------------
     QM CALCULATION INFO
   --------------------------------------------------------------------------------

   | QMMM: Citation for AMBER QMMM Run:
   | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008

   QMMM: SINGLET STATE CALCULATION
   QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132

   | QMMM: *** Selected Hamiltonian *** 
   | QMMM: AM1         

   | QMMM: *** Parameter sets in use ***
   | QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
   | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
   | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
   | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
   | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)

   | QMMM: *** SCF convergence criteria ***
   | QMMM: Energy change                :  0.1D-09 kcal/mol
   | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
   | QMMM: Density matrix change        :  0.5D-06
   | QMMM: Maximum number of SCF cycles :     1000

   | QMMM: *** Diagonalization Routine Information ***
   | QMMM: Pseudo diagonalizations are allowed.
   | QMMM: Auto diagonalization routine selection is in use.
   | QMMM:
   | QMMM: Timing diagonalization routines:
   | QMMM:                              norbs =      217
   | QMMM:    diag iterations used for timing =        4
   | QMMM:
   | QMMM:              Internal diag routine = 0.050281 seconds
   | QMMM:                 Dspev diag routine = 0.043968 seconds
   | QMMM:                Dspevd diag routine = 0.032120 seconds
   | QMMM:                Dspevx diag routine = 0.153124 seconds
   | QMMM:                 Dsyev diag routine = 0.047103 seconds
   | QMMM:                Dsyevd diag routine = 0.033926 seconds
   | QMMM:                Dsyevr diag routine = 0.039887 seconds
   | QMMM:
   | QMMM:                Pseudo diag routine = 0.024004 seconds
   | QMMM:
   | QMMM: Using dspevd routine (diag_routine=3).

     QMMM: QM Region Cartesian Coordinates (*=link atom) 
     QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
     QMMM:     1        1      P       17.4620    0.4650   57.8060
     QMMM:     2        2      O       16.5620   -0.5740   58.3900
     QMMM:     3        3      O       18.0440    0.2210   56.4520
     QMMM:     4        4      O       18.6480    0.7880   58.8450
     QMMM:     5        5      C       18.2700    1.3930   60.1070
     QMMM:     6        6      C       19.4870    1.8540   60.8730
     QMMM:     7        7      O       19.0230    2.6210   62.0160
     QMMM:     8        8      C       20.3910    0.7570   61.4600
     QMMM:     9        9      O       21.7470    1.1830   61.4090
     QMMM:    10       10      C       19.8810    0.6600   62.8920
     QMMM:    11       11      O       20.8230    0.1440   63.8270
     QMMM:    12       12      C       19.6340    2.1310   63.1840
     QMMM:    13       13      N       18.7140    2.3450   64.2950
     QMMM:    14       14      C       17.4200    1.8950   64.3780
     QMMM:    15       15      N       16.8230    2.2310   65.4940
     QMMM:    16       16      C       17.7860    2.9360   66.2020
     QMMM:    17       17      C       17.7680    3.5530   67.4670
     QMMM:    18       18      N       16.7090    3.5600   68.2720
     QMMM:    19       19      N       18.9020    4.1690   67.8780
     QMMM:    20       20      C       19.9640    4.1590   67.0630
     QMMM:    21       21      N       20.0960    3.6140   65.8570
     QMMM:    22       22      C       18.9590    3.0090   65.4750
     QMMM:    23       23      O       16.6940    1.8750   57.8220
     QMMM:    24       24      P       16.8310    3.1760   56.8950
     QMMM:    25       25      O       16.1610    4.3450   57.5500
     QMMM:    26       26      O       18.2590    3.2930   56.4770
     QMMM:    27       27      O       15.9430    2.7150   55.6410
     QMMM:    28       28      C       14.5280    2.4980   55.8770
     QMMM:    29       29      C       13.9670    1.5170   54.8750
     QMMM:    30       30      O       14.0230    2.0920   53.5500
     QMMM:    31       31      C       14.6700    0.1520   54.7880
     QMMM:    32       32      O       13.7350   -0.9120   54.6620
     QMMM:    33       33      C       15.5640    0.2940   53.5490
     QMMM:    34       34      O       15.7840   -0.9330   52.8700
     QMMM:    35       35      C       14.7120    1.2110   52.6690
     QMMM:    36       36      N       15.5520    2.0170   51.7640
     QMMM:    37       37      C       15.9700    1.4830   50.5670
     QMMM:    38       38      C       16.8040    2.2160   49.7300
     QMMM:    39       39      C       17.2170    1.5960   48.4310
     QMMM:    40       40      O       16.7920    0.4660   48.1440
     QMMM:    41       41      N       18.0490    2.2680   47.6420
     QMMM:    42       42      C       17.1960    3.4950   50.0970
     QMMM:    43       43      C       16.7690    4.0240   51.3000
     QMMM:    44       44      C       15.9580    3.2770   52.1340
     QMMM:    45       45      P       20.6860   -1.4490   64.0240
     QMMM:    46       46      O       21.7060   -1.8020   65.0890
     QMMM:    47       47      O       21.0090   -2.0990   62.6800
     QMMM:    48       48      O       19.2630   -1.7280   64.4740
     QMMM:    49       49      H       17.7290    0.6600   60.7060
     QMMM:    50       50      H       17.6220    2.2480   59.9150
     QMMM:    51       51      H       20.0850    2.5010   60.2310
     QMMM:    52       52      H       20.2560   -0.1860   60.9310
     QMMM:    53       53      H       22.3250    0.4250   61.5240
     QMMM:    54       54      H       18.9490    0.0970   62.9320
     QMMM:    55       55      H       20.5770    2.6470   63.3660
     QMMM:    56       56      H       16.9410    1.3200   63.5990
     QMMM:    57       57      H       15.8540    3.1050   67.9850
     QMMM:    58       58      H       16.7600    4.0200   69.1700
     QMMM:    59       59      H       20.8400    4.6670   67.4390
     QMMM:    60       60      H       14.0000    3.4470   55.7840
     QMMM:    61       61      H       14.3870    2.1050   56.8840
     QMMM:    62       62      H       12.9200    1.3420   55.1230
     QMMM:    63       63      H       15.2870   -0.0020   55.6730
     QMMM:    64       64      H       13.8800   -1.5500   55.3640
     QMMM:    65       65      H       16.5100    0.7710   53.8050
     QMMM:    66       66      H       16.3180   -1.5120   53.4190
     QMMM:    67       67      H       13.9980    0.6220   52.0930
     QMMM:    68       68      H       15.6500    0.4930   50.2770
     QMMM:    69       69      H       18.3800    3.1810   47.9180
     QMMM:    70       70      H       18.3500    1.8650   46.7660
     QMMM:    71       71      H       17.8320    4.0750   49.4450
     QMMM:    72       72      H       17.0690    5.0210   51.5890
     QMMM:    73       73      H       15.6420    3.6860   53.0820

   --------------------------------------------------------------------------------
     RESULTS
   --------------------------------------------------------------------------------


   QMMM: ERROR!
   QMMM: Unable to achieve self consistency to the tolerances specified
   QMMM: No convergence in SCF after   1000 steps.
   QMMM: E =  -0.2168E+07 DeltaE =  -0.4757E+03 DeltaP =   0.9525E+00
   QMMM: Smallest DeltaE =   0.8289E-07 DeltaP =   0.1057E-04 Step =      3




Failure running ANTECHAMBER for residue NAP Check reply log for details  

> color bfactor sel

96 atoms, 2 residues, atom bfactor range 41.3 to 73.2  

> select clear

> show #!13 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!13 models

> show #!6 models

> select #14/A:97

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.90725,0.31566,-0.27796,2.8054,0.29785,-0.01556,0.95449,-50.578,0.29696,-0.94875,-0.10814,46.454

> view matrix models
> #14,0.93295,0.28926,-0.21434,-0.73384,0.25781,-0.12123,0.95856,-50.42,0.25129,-0.94954,-0.18768,51.003

> view matrix models
> #14,0.95399,0.10503,0.28085,-26.454,-0.27841,-0.037495,0.95973,-44.999,0.11133,-0.99376,-0.0065275,43.104

> view matrix models
> #14,0.98633,-0.1547,0.056722,-15.368,-0.093531,-0.24224,0.9657,-47.262,-0.13566,-0.9578,-0.2534,58.309

> hide #!6 models

> show #4 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #4 models

> show #5 models

> hide #!6 models

> show #!6 models

> hide #5 models

> select #14/A:60

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.98633,-0.1547,0.056722,5.0516,-0.093531,-0.24224,0.9657,-51.288,-0.13566,-0.9578,-0.2534,64.425

> view matrix models
> #14,0.98633,-0.1547,0.056722,10.913,-0.093531,-0.24224,0.9657,-51.526,-0.13566,-0.9578,-0.2534,63.602

> view matrix models
> #14,0.98633,-0.1547,0.056722,15.905,-0.093531,-0.24224,0.9657,-50.924,-0.13566,-0.9578,-0.2534,60.642

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.97926,-0.18136,0.090283,14.242,-0.086033,0.031182,0.9958,-52.444,-0.18342,-0.98292,0.014932,47.335

> select clear

> select #14/A:91

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view matrix models
> #14,0.90266,-0.17746,0.39205,-0.47885,-0.41831,-0.14782,0.8962,-44.018,-0.10109,-0.97296,-0.20766,57.936

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.90266,-0.17746,0.39205,-2.5843,-0.41831,-0.14782,0.8962,-43.691,-0.10109,-0.97296,-0.20766,52.913

> select clear

> hide #!6 models

> show #!6 models

> select clear

Drag select of 26 atoms, 132 residues, 25 bonds  
Drag select of 40 atoms, 192 residues, 36 bonds  

> hide sel cartoons

> view matrix models
> #14,0.90266,-0.17746,0.39205,-4.6463,-0.41831,-0.14782,0.8962,-41.429,-0.10109,-0.97296,-0.20766,56.964

> select clear

[Repeated 1 time(s)]

> show #!3 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!3 models

> show #!3 models

> select #14/A

3671 atoms, 3705 bonds, 506 residues, 1 model selected  

> show sel cartoons

> select clear

> hide #!3 models

> open 3w78 fromDatabase pdb format mmcif

Summary of feedback from opening 3w78 fetched from pdb  
---  
notes | Fetching compressed mmCIF 3w78 from http://files.rcsb.org/download/3w78.cif  
Fetching CCD CBD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CBD/CBD.cif  
Fetching CCD FMN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/FMN/FMN.cif  

3w78 title:  
Crystal Structure of azoreductase AzrC in complex with NAD(P)-inhibitor
Cibacron Blue [more info...]  

Chain information for 3w78 #15  
---  
Chain | Description | UniProt  
A B C D | FMN-dependent NADH-azoreductase | C0STY1_9BACI 1-211  

Non-standard residues in 3w78 #15  
---  
CBD \u2014 cibacron blue  
FMN \u2014 flavin mononucleotide (riboflavin monophosphate)  

3w78 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  


> matchmaker #15 to #6

Computing secondary structure  
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 fold_azor_monomer_fad_model_0.cif, chain A (#6) with 3w78, chain A
(#15), sequence alignment score = 709.3  
RMSD between 188 pruned atom pairs is 0.720 angstroms; (across all 207 pairs:
1.539)  


> hide #!6 models

> select #15/A

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> select #15/C

1697 atoms, 1735 bonds, 217 residues, 1 model selected  

> select #15/C

1697 atoms, 1735 bonds, 217 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #15/D

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #!3 models

> hide #!14 models

> hide #!3 models

> select #15/A

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> rainbow sel

> select clear

> select #15/B

1696 atoms, 1735 bonds, 216 residues, 1 model selected  

> rainbow sel

> select clear

> show #!3 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> select #3/B:169

11 atoms, 11 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> select clear

> show #15 models

> hide #15 models

> show #15 models

> select #3/B:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 7 atom styles  

> show sel atoms

> hide sel atoms

> select clear

> select #3/A:184

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> show sel atoms

> hide #!3 models

> show #!3 models

> hide #15 models

> select clear

> show #15 models

> select #15/B:52

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #4 models

> hide #4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #15/A:186

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> show sel atoms

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #4 models

> show #!3 models

> hide #4 models

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select clear

> select #15/A

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> show #!3 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #!3 models

> select #15/A

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> select #15/B

1696 atoms, 1735 bonds, 216 residues, 1 model selected  

> color sel light gray

> color sel gray

> select clear

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #15/B:52

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> show sel atoms

> show #!3 models

> hide #!3 models

> show #!3 models

> select #3/A:147

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 12 atom styles  

> show sel atoms

> hide sel atoms

> select clear

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> select #3/B:127

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> show sel atoms

> select clear

> select #3/B:124

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 12 atom styles  

> show sel atoms

> hide #!3 models

> show #!3 models

> select #3/B:122

11 atoms, 11 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> select #3/B:126

5 atoms, 4 bonds, 1 residue, 1 model selected  

> open 4m0C fromDatabase pdb format mmcif

Summary of feedback from opening 4m0C fetched from pdb  
---  
note | Fetching compressed mmCIF 4m0c from http://files.rcsb.org/download/4m0c.cif  

4m0c title:  
The crystal structure of a FMN-dependent NADH-azoreductase from Bacillus
anthracis str. Ames Ancestor in complex with FMN. [more info...]  

Chain information for 4m0c #16  
---  
Chain | Description | UniProt  
A B | FMN-dependent NADH-azoreductase 1 | AZOR1_BACAN 1-220  

Non-standard residues in 4m0c #16  
---  
FMN \u2014 flavin mononucleotide (riboflavin monophosphate)  
GOL \u2014 glycerol (glycerin; propane-1,2,3-triol)  
ZN \u2014 zinc ion  


> hide #15 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #!3 models

> hide #!16 models

> show #15 models

> hide #15 models

> matchmaker #!16 to #3

Computing secondary structure  
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
(#16), sequence alignment score = 530.5  
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)  


> show #!16 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #15 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> select #3/A:24

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> show sel atoms

> select #3/A:28

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> show sel atoms

> show #!16 models

> select #3/A:24@NZ

1 atom, 1 residue, 1 model selected  

> color (#!3 & sel) blue

> select clear

> hide #!3 models

> show #!3 models

> select #3/B:60

14 atoms, 15 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 14 atom styles  

> show sel atoms

> hide #!3 models

> show #!3 models

> hide #!3 models

> color #!16 bypolymer

> color #!16 bychain

> undo

> show #!14 models

> hide #!14 models

> view matrix models
> #3,0.14541,-0.27369,0.95076,11.699,0.94367,-0.25032,-0.21638,-0.059448,0.29722,0.92867,0.22188,0.19931

> view matrix models
> #3,0.14541,-0.27369,0.95076,11.468,0.94367,-0.25032,-0.21638,0.097978,0.29722,0.92867,0.22188,1.1612

> show #!3 models

> hide #!3 models

> view matrix models
> #3,0.14541,-0.27369,0.95076,11.206,0.94367,-0.25032,-0.21638,1.5618,0.29722,0.92867,0.22188,1.9041

> show #!3 models

> hide #!3 models

> show #15 models

> hide #!16 models

> hide #15 models

> show #15 models

> show #!16 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #!16 models

> show #!3 models

> hide #15 models

> view matrix models
> #3,0.14541,-0.27369,0.95076,3.1194,0.94367,-0.25032,-0.21638,-4.132,0.29722,0.92867,0.22188,5.8471

> select #/B

Expected an objects specifier or a keyword  

> select #3/B

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> rainbow sel

> select #3/A:85

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show #5 models

> hide #!3 models

> show #!3 models

> show #!6 models

> hide #5 models

> hide #!3 models

> hide #!6 models

> show #8 models

> rainbow #8

> show #9 models

> hide #9 models

> show #9 models

> hide #8 models

> show #10 models

> hide #9 models

> rainbow #10

> show #9 models

> show #11 models

> hide #11 models

> ui tool show Matchmaker

> matchmaker #8-10 to #7

Computing secondary structure  
[Repeated 3 time(s)]  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 fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56  
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)  

Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5  
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)  

Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2  
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)  


> view matrix models
> #3,0.14541,-0.27369,0.95076,8.5292,0.94367,-0.25032,-0.21638,-19.372,0.29722,0.92867,0.22188,0.15815

> hide #9 models

> show #11 models

> hide #10 models

> show #12 models

> hide #11 models

> hide #12 models

> show #7 models

> rainbow #7

> show #8 models

> hide #7 models

> show #7 models

> hide #8 models

> show #5 models

> hide #5 models

> show #!6 models

> hide #7 models

> show #7 models

> hide #!6 models

> show #!6 models

> hide #7 models

> show #7 models

> select #7/A:182

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.056929,0.94842,-0.31187,29.698,-0.99216,0.018927,-0.12355,27.519,-0.11127,0.31646,0.94206,-48.931

> ui mousemode right "rotate selected models"

> select #7/A:168

11 atoms, 11 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.6578,0.45453,-0.60058,25.727,0.50261,-0.85878,-0.099448,19.133,-0.56096,-0.23644,-0.79336,-49.882

> view matrix models
> #7,0.60118,0.48068,-0.63838,25.96,0.54786,-0.82948,-0.10864,18.796,-0.58175,-0.28444,-0.76201,-49.624

> view matrix models
> #7,0.49131,0.84301,-0.21895,27.321,0.79014,-0.53716,-0.29517,16.511,-0.36645,-0.027978,-0.93002,-51.657

> view matrix models
> #7,0.29276,0.89319,-0.34133,28.206,0.88387,-0.38897,-0.25975,15.859,-0.36478,-0.22565,-0.90334,-51.396

> view matrix models
> #7,0.39394,0.66509,-0.6344,27.076,0.74669,-0.63405,-0.20106,17.118,-0.53597,-0.3945,-0.7464,-49.757

> view matrix models
> #7,0.3975,0.64273,-0.6549,27.026,0.73208,-0.65243,-0.19596,17.242,-0.55323,-0.40155,-0.72986,-49.601

> view matrix models
> #7,0.31312,0.65044,-0.69202,27.453,0.7722,-0.59855,-0.21318,16.892,-0.55286,-0.46763,-0.68969,-49.434

> view matrix models
> #7,0.41324,0.50876,-0.75524,26.815,0.7267,-0.68404,-0.06317,17.64,-0.54875,-0.52273,-0.6524,-49.31

> select clear

> hide #7 models

> show #8 models

> select #8/A:495

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.29707,0.95019,0.094245,27.561,-0.9516,-0.28647,-0.11132,28.24,-0.078773,-0.12275,0.98931,-51.568

> ui mousemode right "rotate selected models"

> select #8/A:464

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view matrix models
> #8,-0.83282,-0.06747,-0.54942,33.938,0.53295,-0.36591,-0.76293,29.175,-0.14956,-0.9282,0.3407,-46.42

> view matrix models
> #8,-0.79413,0.58208,0.17476,27.984,0.60087,0.79512,0.08207,22.702,-0.09118,0.17018,-0.98119,-32.86

> view matrix models
> #8,-0.74237,-0.25474,0.61968,22.54,0.1102,0.86588,0.48796,20.688,-0.66087,0.43053,-0.61473,-33.983

> view matrix models
> #8,-0.85203,0.52313,0.019577,29.536,0.49615,0.81887,-0.28859,26.523,-0.167,-0.23617,-0.95725,-33.383

> view matrix models
> #8,-0.82201,-0.085732,0.56298,23.565,0.39872,0.61921,0.67646,17.631,-0.4066,0.78053,-0.47481,-35.657

> view matrix models
> #8,-0.96452,-0.0076278,0.26388,26.924,0.094374,0.92356,0.37165,21.898,-0.24655,0.38337,-0.89008,-32.89

> view matrix models
> #8,-0.97869,-0.027577,0.20348,27.504,0.057976,0.91351,0.40267,21.719,-0.19698,0.40588,-0.89245,-33.004

> view matrix models
> #8,-0.96042,0.18076,0.21192,27.65,0.26575,0.82255,0.50278,19.967,-0.083434,0.5392,-0.83803,-33.708

> view matrix models
> #8,-0.94381,0.13924,0.29972,26.723,0.29173,0.77716,0.5576,19.31,-0.15529,0.61371,-0.77411,-33.957

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs

> hide #8 models

> show #!13 models

> hide #!13 models

> show #!14 models

> hide #!14 models

> show #!16 models

> open 1v4B fromDatabase pdb format mmcif

Summary of feedback from opening 1v4B fetched from pdb  
---  
notes | Fetching compressed mmCIF 1v4b from http://files.rcsb.org/download/1v4b.cif  
Fetching CCD IPA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/IPA/IPA.cif  

1v4b title:  
The crystal structure of AzoR (Azo Reductase) from Escherichia coli: Oxidized
form [more info...]  

Chain information for 1v4b #17  
---  
Chain | Description | UniProt  
A | NADH-azoreductase, FMN-dependent | ACPD_ECOLI 1-200  

Non-standard residues in 1v4b #17  
---  
EDO \u2014 1,2-ethanediol (ethylene glycol)  
FMN \u2014 flavin mononucleotide (riboflavin monophosphate)  
IPA \u2014 isopropyl alcohol (2-propanol)  

1v4b mmCIF Assemblies  
---  
1| author_defined_assembly  


> open 2B3D fromDatabase pdb format mmcif

Summary of feedback from opening 2B3D fetched from pdb  
---  
note | Fetching compressed mmCIF 2b3d from http://files.rcsb.org/download/2b3d.cif  

2b3d title:  
Crystal structure of Modulator of Drug activity B in complex with flavin
adenine dinucleotide [more info...]  

Chain information for 2b3d #18  
---  
Chain | Description | UniProt  
A B | Modulator of drug activity B | MDAB_ECOLI 13-204  

Non-standard residues in 2b3d #18  
---  
FAD \u2014 flavin-adenine dinucleotide  


> hide #!16 models

> hide #!17 models

> matchmaker #!18 to #3

Computing secondary structure  
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain B
(#18), sequence alignment score = 156.9  
RMSD between 82 pruned atom pairs is 1.158 angstroms; (across all 168 pairs:
6.190)  


> show #!3 models

> hide #!6 models

> hide #!3 models

> show #!3 models

> hide #!18 models

> show #!6 models

> select /A

43169 atoms, 43600 bonds, 3 pseudobonds, 5896 residues, 20 models selected  

> hide #!3 models

> show #!3 models

> show #7 models

> hide #7 models

> hide #!6 models

> matchmaker #1,4-5,7-12,15#!2,6,13-14,16-18 & sel to #3 & sel

Computing secondary structure  
[Repeated 12 time(s)]  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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1081.4  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1081.4  
RMSD between 208 pruned atom pairs is 0.436 angstroms; (across all 208 pairs:
0.436)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1085  
RMSD between 208 pruned atom pairs is 0.263 angstroms; (across all 208 pairs:
0.263)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1081.4  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1074.2  
RMSD between 208 pruned atom pairs is 0.269 angstroms; (across all 208 pairs:
0.269)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 83.4  
RMSD between 10 pruned atom pairs is 1.453 angstroms; (across all 169 pairs:
23.782)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 59.8  
RMSD between 7 pruned atom pairs is 1.684 angstroms; (across all 65 pairs:
22.736)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 65.4  
RMSD between 24 pruned atom pairs is 1.163 angstroms; (across all 154 pairs:
32.226)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 59.3  
RMSD between 31 pruned atom pairs is 1.111 angstroms; (across all 142 pairs:
21.293)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2  
RMSD between 6 pruned atom pairs is 1.325 angstroms; (across all 101 pairs:
17.171)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 9h2i, chain A
(#13), sequence alignment score = 24  
RMSD between 11 pruned atom pairs is 0.322 angstroms; (across all 26 pairs:
11.957)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 8rx4, chain A
(#14), sequence alignment score = 51.5  
RMSD between 10 pruned atom pairs is 1.029 angstroms; (across all 173 pairs:
29.959)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 3w78, chain A
(#15), sequence alignment score = 716.5  
RMSD between 189 pruned atom pairs is 0.774 angstroms; (across all 207 pairs:
1.461)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
(#16), sequence alignment score = 530.5  
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 1v4b, chain A
(#17), sequence alignment score = 427.4  
RMSD between 135 pruned atom pairs is 1.176 angstroms; (across all 194 pairs:
2.701)  

Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain A
(#18), sequence alignment score = 150.4  
RMSD between 82 pruned atom pairs is 1.208 angstroms; (across all 167 pairs:
6.224)  


> show #!6 models

> hide #!6 models

> show #!18 models

> hide #!3 models

> show #!3 models

> hide #!18 models

> show #!6 models

> show #!2 models

> hide #!6 models

> show #!6 models

> hide #!2 models

> hide #!3 models

> show #!18 models

> hide #!18 models

> show #!17 models

> show #!16 models

> hide #!16 models

> show #!18 models

> hide #!17 models

> view matrix models
> #1,0.84943,0.0048481,-0.52768,0.65374,-0.36539,0.72688,-0.5815,-14.996,0.38074,0.68675,0.6192,0.19483,#6,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#11,0.3554,0.83707,0.41595,-1.2763,0.68382,0.070534,-0.72623,-14.22,-0.63724,0.54254,-0.54734,0.48453,#2,-0.46068,-0.87689,-0.13724,12.214,-0.014771,-0.14703,0.98902,-16.145,-0.88745,0.45765,0.054778,1.5059,#3,-0.028746,-0.72374,0.68947,11.158,0.45997,-0.62197,-0.6337,-18.381,0.88747,0.29892,0.35078,3.9374,#4,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#5,0.22887,-0.90083,-0.36896,11.233,0.86356,0.36282,-0.35017,-15.736,0.44931,-0.23848,0.86096,4.0367,#7,0.46353,0.81912,0.33791,5.0029,-0.6474,0.57345,-0.50202,-21.729,-0.60499,0.013936,0.79611,6.3283,#8,-0.26206,-0.91936,-0.29342,-0.19912,0.46009,0.14825,-0.87541,-25.028,0.84832,-0.36441,0.38414,-10.304,#9,-0.36876,-0.75997,0.53522,0.42258,-0.57013,0.63969,0.5155,-25.953,-0.73415,-0.11505,-0.66917,-11.957,#10,-0.76439,0.47517,0.4358,-2.938,-0.63904,-0.46854,-0.60999,-30.867,-0.085662,-0.74477,0.6618,-2.3478,#12,0.5306,0.7007,0.47695,28.271,0.79647,-0.60467,0.0022843,-13.278,0.29,0.37867,-0.87893,-22.901,#13,-0.87207,0.20936,-0.44234,-12.953,-0.35472,-0.89312,0.27661,-70.145,-0.33715,0.39813,0.85313,-58.476,#14,0.06735,0.64492,0.76128,-46.484,-0.9052,0.36039,-0.22523,-11.844,-0.41961,-0.67394,0.60805,-31.123,#15,-0.96531,0.14882,-0.21456,-77.459,0.24373,0.21868,-0.94487,-1.6269,-0.093694,-0.96438,-0.24737,25.022,#16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786,#17,0.86185,-0.43699,0.25741,-7.1671,0.16099,0.71702,0.67821,-60.106,-0.48094,-0.54307,0.68831,13.982,#18,-0.37684,0.76002,-0.52949,10.529,0.34458,-0.41558,-0.84176,-4.7032,-0.8598,-0.49966,-0.10528,11.963

> show #1 models

> hide #!6 models

> hide #!18 models

> show #!6 models

> hide #1 models

> show #!3 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select clear

> show #1 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #4 models

> hide #1 models

> show #!3 models

> hide #4 models

> show #1 models

> hide #!3 models

> show #!17 models

> hide #!17 models

> show #!18 models

> hide #1 models

> show #1 models

> show #!3 models

> hide #1 models

> hide #!3 models

> show #1 models

> hide #1 models

> select ::name="FAD"

477 atoms, 522 bonds, 9 residues, 6 models selected  

> show #!6 models

> hide #!6 models

> color sel & #!18 bychain

> undo

> select clear

> color #!18 bychain

> undo

> show #!3 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!18 models

> hide #!3 models

> show #!3 models

> hide #!18 models

> show #!18 models

> hide #!3 models

> show #!6 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!3 models

> hide #!3 models

> show #!18 models

> show #1 models

> hide #!6 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!3 models

> hide #1 models

> select #3/A

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> select ::name="FAD"

477 atoms, 522 bonds, 9 residues, 6 models selected  

> select ~sel & ##selected

25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected  

> ui tool show "Color Actions"

> color sel tan

> color sel goldenrod

> select #3/B

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> rainbow sel

> select clear

> select ::name="FAD"

477 atoms, 522 bonds, 9 residues, 6 models selected  

> select ~sel & ##selected

25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected  

> color sel dark goldenrod

> color sel salmon

> color sel dark goldenrod

> color sel peru

> color sel dark orange

> color sel saddle brown

> color sel dark goldenrod

> color sel slate gray

> color sel steel blue

> color sel cadet blue

> color sel dark olive green

> select #3/B

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> rainbow sel

> select clear

> show #1 models

> hide #!3 models

> show #!13 models

> hide #!13 models

> show #!6 models

> hide #1 models

> show #1 models

> hide #!6 models

> show #4 models

> hide #1 models

> show #1 models

> hide #4 models

> show #4 models

> hide #1 models

> show #!3 models

> hide #!3 models

> show #1 models

> hide #4 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.png width
> 600 height 489 supersample 4 transparentBackground true

> show #4 models

> hide #1 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR-FAD.png
> width 600 height 489 supersample 4 transparentBackground true

> show #!3 models

> hide #4 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.png
> width 600 height 489 supersample 4 transparentBackground true

> select #3/A

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> show sel surfaces

> select clear

> select #3/B

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> hide #!3 models

> show #1 models

> show #!6 models

> hide #1 models

> show #1 models

> show #!3 models

> hide #!6 models

> hide #1 models

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.s.png
> width 600 height 489 supersample 4 transparentBackground true

> show #11 models

> hide #!3 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #12 models

> hide #12 models

> show #!6 models

> hide #11 models

> show #!2 models

> show #!3 models

> hide #!2 models

> hide #!6 models

> hide #!3 surfaces

> select add #3/B:123

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:122

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.png
> width 600 height 489 supersample 4 transparentBackground true

> select #3/B:123

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:122

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select add #3/B:124

23 atoms, 23 bonds, 2 residues, 2 models selected  

> select add #3/A:148

35 atoms, 35 bonds, 3 residues, 2 models selected  

> select add #3/A:184

43 atoms, 42 bonds, 4 residues, 3 models selected  

> select add #3/A:101@CA

44 atoms, 42 bonds, 5 residues, 3 models selected  

> select add #3/A:102@CB

45 atoms, 43 bonds, 6 residues, 3 models selected  

> select subtract #3/A:102

44 atoms, 43 bonds, 5 residues, 3 models selected  

> select add #3/A:102

52 atoms, 50 bonds, 6 residues, 3 models selected  

> select subtract #3/A:101

51 atoms, 49 bonds, 5 residues, 3 models selected  

> select add #3/A:101

59 atoms, 56 bonds, 6 residues, 3 models selected  

> select add #3/A:100

73 atoms, 71 bonds, 7 residues, 3 models selected  

> select add #3/A:99

81 atoms, 78 bonds, 8 residues, 3 models selected  

> select add #3/A:183

91 atoms, 88 bonds, 9 residues, 3 models selected  

> select add #3/A:143

97 atoms, 93 bonds, 10 residues, 3 models selected  

> select add #3/A:98

104 atoms, 100 bonds, 11 residues, 3 models selected  

> select add #3/A:19

110 atoms, 105 bonds, 12 residues, 3 models selected  

> select add #3/A:18

118 atoms, 112 bonds, 13 residues, 3 models selected  

> select add #3/A:17

124 atoms, 117 bonds, 14 residues, 3 models selected  

> select add #3/A:16

131 atoms, 123 bonds, 15 residues, 3 models selected  

> select add #3/A:9

136 atoms, 127 bonds, 16 residues, 3 models selected  

> select subtract #3/A:9

131 atoms, 123 bonds, 15 residues, 3 models selected  

> select add #3/A:8

138 atoms, 129 bonds, 16 residues, 3 models selected  

> select subtract #3/A:8

131 atoms, 123 bonds, 15 residues, 3 models selected  

> select add #3/A:10@CB

132 atoms, 123 bonds, 16 residues, 3 models selected  

> select subtract #3/A:10@CB

131 atoms, 123 bonds, 15 residues, 3 models selected  

> select add #3/A:10

141 atoms, 133 bonds, 16 residues, 3 models selected  

> select add #3/B:57

149 atoms, 140 bonds, 17 residues, 3 models selected  

> select add #3/B:52

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CG

158 atoms, 147 bonds, 19 residues, 3 models selected  

> select subtract #3/B:60@CG

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CG

158 atoms, 147 bonds, 19 residues, 3 models selected  

> select subtract #3/B:60@CG

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CG

158 atoms, 148 bonds, 19 residues, 3 models selected  

> select subtract #3/B:60@CG

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select subtract #3/B:52

149 atoms, 140 bonds, 17 residues, 3 models selected  

> select add #3/B:52

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CG

158 atoms, 147 bonds, 19 residues, 3 models selected  

> select subtract #3/B:60@CG

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CB

158 atoms, 147 bonds, 19 residues, 3 models selected  

> label (#!3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select #3/B:197

6 atoms, 5 bonds, 1 residue, 1 model selected  

> label height 3

> label height 2

> label height 1

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true

> show #5 models

> hide #!3 models

> select #5/B:123

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5/B:122

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select add #5/B:124

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select add #5/A:100

37 atoms, 39 bonds, 3 residues, 1 model selected  

> select add #5/A:101

45 atoms, 45 bonds, 4 residues, 1 model selected  

> select add #5/A:16

52 atoms, 51 bonds, 5 residues, 1 model selected  

> select add #5/A:10

62 atoms, 61 bonds, 6 residues, 1 model selected  

> select add #5/A:11

69 atoms, 68 bonds, 7 residues, 1 model selected  

> select subtract #5/A:11

62 atoms, 61 bonds, 6 residues, 1 model selected  

> select add #5/A:12

73 atoms, 72 bonds, 7 residues, 1 model selected  

> select add #5/B:60

87 atoms, 87 bonds, 8 residues, 1 model selected  

> select add #5/B:57

95 atoms, 94 bonds, 9 residues, 1 model selected  

> select add #5/B:58

102 atoms, 100 bonds, 10 residues, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> label height 1

[Repeated 1 time(s)]

> select clear

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #5/B:113

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> show sel atoms

> show #4 models

> hide #4 models

> show #!3 models

> hide #!5 models

> show #4 models

> hide #4 models

> show #!5 models

> hide #!3 models

> hide sel atoms

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true

> hide #!5 models

> show #7 models

> hide #7 models

> show #11 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> select add #11/A:101

8 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #11/A:143

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select add #11/A:19

20 atoms, 18 bonds, 3 residues, 1 model selected  

> select add #11/A:18

28 atoms, 25 bonds, 4 residues, 1 model selected  

> select add #11/A:17

34 atoms, 30 bonds, 5 residues, 1 model selected  

> select add #11/A:10

44 atoms, 40 bonds, 6 residues, 1 model selected  

> select add #11/A:100

58 atoms, 55 bonds, 7 residues, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> label height 1

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_NAD.png
> width 600 height 489 supersample 4 transparentBackground true

> show #!5 models

> hide #!11 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true

> ~label #5 residues

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.png
> width 600 height 489 supersample 4 transparentBackground true

> show #15 models

> hide #5 models

> show #4 models

> hide #4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select ::name="CBD"

204 atoms, 224 bonds, 4 residues, 1 model selected  

> color sel pale turquoise

> select clear

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/3w78.AzrC.CBD.FMN.png
> width 600 height 489 supersample 4 transparentBackground true

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #15 models

> select #3/B:126

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show #15 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> select #15/B:60

14 atoms, 15 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 14 atom styles  

> show sel atoms

> select clear

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #15 models

> undo

> hide #!16 models

> show #!16 models

> hide #15 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs

> show #!6 models

> hide #!16 models

> show #1 models

> hide #!6 models

> show #!16 models

> hide #1 models

> show #!6 models

> hide #!16 models

> show #!16 models

> hide #!6 models

> show #1 models

> hide #!16 models

> show #!16 models

> hide #1 models

> show #!3 models

> hide #!16 models

> show #!16 models

> hide #!3 models

> select #16/B:126

6 atoms, 5 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 6 atom styles  

> show sel atoms

> show #5 models

> hide #5 models

> show #!17 models

> hide #!16 models

> show #1 models

> show #!3 models

> hide #!3 models

> show #!6 models

> hide #1 models

> hide #!6 models

> show #!6 models

> show #!3 models

> hide #!6 models

> hide #!17 models

> show #15 models

> hide #!3 models

> show #!16 models

> hide #15 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!16 models

> show #!3 models

> show #1 models

> hide #1 models

> show #7 models

> hide #7 models

> hide #!6 models

> show #1 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #!6 models

> hide #!6 models

> hide #1 models

> show #7 models

> show #1 models

> hide #7 models

> show #7 models

> hide #1 models

> show #8 models

> hide #8 models

> show #8 models

> hide #7 models

> view matrix models
> #16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786

> hide #8 models

> show #12 models

> hide #12 models

> show #9 models

> show #10 models

> hide #9 models

> show #!3 models

> hide #10 models

> select #3/A:104

11 atoms, 11 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> show #1 models

> hide #!3 models

> show #!3 models

> hide #1 models

> show #1 models

> hide #!3 models

> show #!3 models

> hide #1 models

> view matrix models
> #3,0.23414,-0.80222,0.54921,11.186,0.21867,-0.50698,-0.83376,-19.133,0.94729,0.31531,0.056721,3.3647

> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159

> open 2Bzs fromDatabase pdb format mmcif

Summary of feedback from opening 2Bzs fetched from pdb  
---  
notes | Fetching compressed mmCIF 2bzs from http://files.rcsb.org/download/2bzs.cif  
Fetching CCD CB1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/CB1/CB1.cif  

2bzs title:  
Binding of anti-cancer prodrug CB1954 to the activating enzyme NQO2 revealed
by the crystal structure of their complex. [more info...]  

Chain information for 2bzs #19  
---  
Chain | Description | UniProt  
A B | NRH DEHYDROGENASE [QUINONE] 2 | NQO2_HUMAN 1-230  

Non-standard residues in 2bzs #19  
---  
CB1 \u2014 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954; Tretazicar)  
FAD \u2014 flavin-adenine dinucleotide  
ZN \u2014 zinc ion  


> hide #!3 models

> color #!19 bychain

> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159

> show #!3 models

> hide #!3 models

> select #3/A

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> matchmaker #!19 to #3 & sel

Computing secondary structure  
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2bzs, chain B
(#19), sequence alignment score = 223.4  
RMSD between 70 pruned atom pairs is 1.017 angstroms; (across all 198 pairs:
5.647)  


> show #!3 models

> select clear

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #1 models

> hide #!19 models

> select #3/A

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> matchmaker #1 to #3 & sel

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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  


> show #!19 models

> hide #1 models

> show #1 models

> hide #!3 models

> hide #!19 models

> show #!19 models

> select #19/B

2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected  

> rainbow sel

> hide #1 models

> show #4 models

> hide #4 models

> show #1 models

> select #19/B

2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected  

> color sel bychain

> select clear

> hide #1 models

> show #!3 models

> hide #!3 models

> show #4 models

> show #!3 models

> hide #4 models

> hide #!19 models

> show #!19 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #1 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!19 models

> select clear

> open 2VPw fromDatabase pdb format mmcif

Summary of feedback from opening 2VPw fetched from pdb  
---  
notes | Fetching compressed mmCIF 2vpw from http://files.rcsb.org/download/2vpw.cif  
Fetching CCD MGD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MGD/MGD.cif  
Fetching CCD MO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/MO/MO.cif  
Fetching CCD MQ7 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/7/MQ7/MQ7.cif  

2vpw title:  
Polysulfide reductase with bound menaquinone [more info...]  

Chain information for 2vpw #20  
---  
Chain | Description | UniProt  
A E | THIOSULFATE REDUCTASE | Q72LA4_THET2 1-765  
B F | NRFC PROTEIN | Q72LA5_THET2 1-195  
C G | HYPOTHETICAL MEMBRANE SPANNING PROTEIN | Q72LA6_THET2 0-252 1-253  

Non-standard residues in 2vpw #20  
---  
MGD \u2014
2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-
anthracen-4-one guanosine dinucleotide (molybdopterin guanosine dinucleotide)  
MO \u2014 molybdenum atom  
MQ7 \u2014 menaquinone-7  
SF4 \u2014 iron/sulfur cluster  


> hide #!19 models

> hide #1 models

> hide #!20 surfaces

[Repeated 1 time(s)]

> hide #!20 atoms

> show #!20 cartoons

> matchmaker #!20 to #3 & sel

No 'to' model specified  

> matchmaker #!20 to #3

Computing secondary structure  
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2vpw, chain E
(#20), sequence alignment score = 78  
RMSD between 8 pruned atom pairs is 1.398 angstroms; (across all 148 pairs:
20.313)  


> show #!3 models

> hide #!3 models

> select /A

51617 atoms, 51746 bonds, 16 pseudobonds, 7421 residues, 24 models selected  

> rainbow sel & #!20

> select ::name="MQ7"

30 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel surfaces

> open 7NZ1 fromDatabase pdb format mmcif

Summary of feedback from opening 7NZ1 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7nz1 from http://files.rcsb.org/download/7nz1.cif  
Fetching CCD CSX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/CSX/CSX.cif  

7nz1 title:  
Respiratory complex I from Escherichia coli - focused refinement of
cytoplasmic arm [more info...]  

Chain information for 7nz1 #21  
---  
Chain | Description | UniProt  
B | NADH-quinone oxidoreductase subunit B |   
D | NADH-quinone oxidoreductase subunit C/D | NUOCD_ECOLI 1-596  
E | NADH-quinone oxidoreductase subunit E | NUOE_ECOLI 1-166  
F | NADH-quinone oxidoreductase subunit F | NUOF_ECOLI 1-445  
G | NADH-quinone oxidoreductase subunit G | NUOG_ECOLI 1-908  
I | NADH-quinone oxidoreductase subunit I | NUOI_ECOLI 1-180  

Non-standard residues in 7nz1 #21  
---  
CA \u2014 calcium ion  
FES \u2014 FE2/S2 (inorganic) cluster  
FMN \u2014 flavin mononucleotide (riboflavin monophosphate)  
SF4 \u2014 iron/sulfur cluster  


> hide sel atoms

> show sel cartoons

> hide #!20 models

> show #!21 cartoons

> hide #!21 atoms

> view matrix models
> #20,-0.20963,0.97025,0.12114,-159.27,0.41872,0.20104,-0.88558,-19.075,-0.88359,-0.13493,-0.44841,140.58

> color #!21 bychain

> matchmaker #!21 to #1

Computing secondary structure  
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 fold_azor_monomer_model_0.cif, chain A (#1) with 7nz1, chain G
(#21), sequence alignment score = 86.3  
RMSD between 22 pruned atom pairs is 0.859 angstroms; (across all 180 pairs:
20.357)  


> show #1 models

> select #21/G

7630 atoms, 7235 bonds, 24 pseudobonds, 1469 residues, 2 models selected  

> rainbow sel

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!21 models

> show #!21 models

> hide #1 models

> matchmaker #!21 to #8

Computing secondary structure  
[Repeated 1 time(s)]  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 fold_mqo_model_0.cif, chain A (#8) with 7nz1, chain G (#21),
sequence alignment score = 63.6  
RMSD between 5 pruned atom pairs is 1.257 angstroms; (across all 362 pairs:
31.062)  


> show #8 models

> hide #!21 models

> hide #8 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_4.cif

Chain information for fold_tcr_ankkflltv_model_0.cif #22  
---  
Chain | Description  
A | .  
B | .  
C | .  

Chain information for fold_tcr_ankkflltv_model_1.cif #23  
---  
Chain | Description  
A | .  
B | .  
C | .  

Chain information for fold_tcr_ankkflltv_model_2.cif #24  
---  
Chain | Description  
A | .  
B | .  
C | .  

Chain information for fold_tcr_ankkflltv_model_3.cif #25  
---  
Chain | Description  
A | .  
B | .  
C | .  

Chain information for fold_tcr_ankkflltv_model_4.cif #26  
---  
Chain | Description  
A | .  
B | .  
C | .  

Computing secondary structure  
[Repeated 4 time(s)]

> ui tool show Matchmaker

> matchmaker #23-26 to #22

Computing secondary structure  
[Repeated 4 time(s)]  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 fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_1.cif, chain B (#23), sequence alignment score = 581  
RMSD between 111 pruned atom pairs is 0.184 angstroms; (across all 111 pairs:
0.184)  

Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_2.cif, chain B (#24), sequence alignment score =
573.8  
RMSD between 111 pruned atom pairs is 0.232 angstroms; (across all 111 pairs:
0.232)  

Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_3.cif, chain B (#25), sequence alignment score = 581  
RMSD between 111 pruned atom pairs is 0.364 angstroms; (across all 111 pairs:
0.364)  

Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_4.cif, chain B (#26), sequence alignment score =
573.8  
RMSD between 110 pruned atom pairs is 0.269 angstroms; (across all 111 pairs:
0.332)  


> view matrix models
> #21,0.56571,0.78878,0.24042,-111.9,-0.81332,0.5818,0.0049461,-39.828,-0.13598,-0.19834,0.97066,-77.181

Drag select of 9 atoms, 113 residues, 8 bonds  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_4.cif

Chain information for fold_tcr_demefteae_model_0.cif #27  
---  
Chain | Description  
A | .  
B | .  
C | .  

Chain information for fold_tcr_demefteae_model_1.cif #28  
---  
Chain | Description  
A | .  
B | .  
C | .  

Chain information for fold_tcr_demefteae_model_2.cif #29  
---  
Chain | Description  
A | .  
B | .  
C | .  

Chain information for fold_tcr_demefteae_model_3.cif #30  
---  
Chain | Description  
A | .  
B | .  
C | .  

Chain information for fold_tcr_demefteae_model_4.cif #31  
---  
Chain | Description  
A | .  
B | .  
C | .  

Computing secondary structure  
[Repeated 4 time(s)]

> matchmaker #27-31 to #22

Computing secondary structure  
[Repeated 5 time(s)]  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 fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_0.cif, chain B (#27), sequence alignment score = 581  
RMSD between 111 pruned atom pairs is 0.323 angstroms; (across all 111 pairs:
0.323)  

Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_1.cif, chain B (#28), sequence alignment score =
570.2  
RMSD between 111 pruned atom pairs is 0.204 angstroms; (across all 111 pairs:
0.204)  

Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_2.cif, chain B (#29), sequence alignment score =
573.8  
RMSD between 111 pruned atom pairs is 0.345 angstroms; (across all 111 pairs:
0.345)  

Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_3.cif, chain B (#30), sequence alignment score = 581  
RMSD between 111 pruned atom pairs is 0.287 angstroms; (across all 111 pairs:
0.287)  

Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_4.cif, chain B (#31), sequence alignment score =
573.8  
RMSD between 111 pruned atom pairs is 0.349 angstroms; (across all 111 pairs:
0.349)  


> select clear

> delete atoms #22-31

> delete bonds #22-31

> show #!13 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs

\u2014\u2014\u2014 End of log from Wed Mar 11 15:25:43 2026 \u2014\u2014\u2014

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

   Hardware Overview:

     Model Name: MacBook Pro
     Model Identifier: MacBookPro18,3
     Model Number: Z15H00105LL/A
     Chip: Apple M1 Pro
     Total Number of Cores: 10 (8 performance and 2 efficiency)
     Memory: 32 GB
     System Firmware Version: 11881.140.96
     OS Loader Version: 11881.140.96

Software:

   System Software Overview:

     System Version: macOS 15.6.1 (24G90)
     Kernel Version: Darwin 24.6.0
     Time since boot: 216 days, 2 hours, 57 minutes

Graphics/Displays:

   Apple M1 Pro:

     Chipset Model: Apple M1 Pro
     Type: GPU
     Bus: Built-In
     Total Number of Cores: 16
     Vendor: Apple (0x106b)
     Metal Support: Metal 3
     Displays:
       DELL U2718Q:
         Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
         UI Looks like: 1920 x 1080 @ 60.00Hz
         Main Display: Yes
         Mirror: Off
         Online: Yes
         Rotation: Supported


Installed Packages:
   alabaster: 1.0.0
   anyio: 4.7.0
   appdirs: 1.4.4
   appnope: 0.1.4
   asttokens: 3.0.0
   auditwheel: 6.1.0
   babel: 2.16.0
   beautifulsoup4: 4.12.3
   blockdiag: 3.0.0
   blosc2: 3.0.0
   build: 1.2.1
   certifi: 2023.11.17
   cftime: 1.6.4.post1
   charset-normalizer: 3.4.0
   ChimeraX-AddCharge: 1.5.18
   ChimeraX-AddH: 2.2.6
   ChimeraX-AlignmentAlgorithms: 2.0.2
   ChimeraX-AlignmentHdrs: 3.5
   ChimeraX-AlignmentMatrices: 2.1
   ChimeraX-Alignments: 2.16.1
   ChimeraX-AlphaFold: 1.0.1
   ChimeraX-AltlocExplorer: 1.1.2
   ChimeraX-AmberInfo: 1.0
   ChimeraX-Arrays: 1.1
   ChimeraX-Atomic: 1.58.8
   ChimeraX-AtomicLibrary: 14.1.11
   ChimeraX-AtomSearch: 2.0.1
   ChimeraX-AxesPlanes: 2.4
   ChimeraX-BasicActions: 1.1.2
   ChimeraX-BILD: 1.0
   ChimeraX-BlastProtein: 3.0.0
   ChimeraX-BondRot: 2.0.4
   ChimeraX-BugReporter: 1.0.1
   ChimeraX-BuildStructure: 2.13.1
   ChimeraX-Bumps: 1.0
   ChimeraX-BundleBuilder: 1.4.0
   ChimeraX-ButtonPanel: 1.0.1
   ChimeraX-CageBuilder: 1.0.1
   ChimeraX-CellPack: 1.0
   ChimeraX-Centroids: 1.4
   ChimeraX-ChangeChains: 1.1
   ChimeraX-CheckWaters: 1.4
   ChimeraX-ChemGroup: 2.0.1
   ChimeraX-Clashes: 2.3
   ChimeraX-ColorActions: 1.0.5
   ChimeraX-ColorGlobe: 1.0
   ChimeraX-ColorKey: 1.5.6
   ChimeraX-CommandLine: 1.2.5
   ChimeraX-ConnectStructure: 2.0.1
   ChimeraX-Contacts: 1.0.1
   ChimeraX-Core: 1.9
   ChimeraX-CoreFormats: 1.2
   ChimeraX-coulombic: 1.4.4
   ChimeraX-Crosslinks: 1.0
   ChimeraX-Crystal: 1.0
   ChimeraX-CrystalContacts: 1.0.1
   ChimeraX-DataFormats: 1.2.3
   ChimeraX-Dicom: 1.2.6
   ChimeraX-DistMonitor: 1.4.2
   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: 1.4.1
   ChimeraX-Hbonds: 2.5
   ChimeraX-Help: 1.3
   ChimeraX-HKCage: 1.3
   ChimeraX-IHM: 1.1
   ChimeraX-ImageFormats: 1.2
   ChimeraX-IMOD: 1.0
   ChimeraX-IO: 1.0.3
   ChimeraX-ItemsInspection: 1.0.1
   ChimeraX-IUPAC: 1.0
   ChimeraX-KVFinder: 1.2.1
   ChimeraX-Label: 1.1.14
   ChimeraX-ListInfo: 1.2.2
   ChimeraX-Log: 1.2
   ChimeraX-LookingGlass: 1.1
   ChimeraX-Maestro: 1.9.1
   ChimeraX-Map: 1.3
   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: 2.1.6
   ChimeraX-MCopy: 1.0
   ChimeraX-MDcrds: 2.7.2
   ChimeraX-MedicalToolbar: 1.1
   ChimeraX-Meeting: 1.0.1
   ChimeraX-MLP: 1.1.1
   ChimeraX-mmCIF: 2.14.2
   ChimeraX-MMTF: 2.2
   ChimeraX-ModelArchive: 1.0
   ChimeraX-Modeller: 1.5.18
   ChimeraX-ModelPanel: 1.5
   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-MutationScores: 1.0
   ChimeraX-Neuron: 1.0
   ChimeraX-Nifti: 1.2
   ChimeraX-NMRSTAR: 1.0.2
   ChimeraX-NRRD: 1.2
   ChimeraX-Nucleotides: 2.0.3
   ChimeraX-OpenCommand: 1.14
   ChimeraX-OrthoPick: 1.0.1
   ChimeraX-PDB: 2.7.6
   ChimeraX-PDBBio: 1.0.1
   ChimeraX-PDBLibrary: 1.0.4
   ChimeraX-PDBMatrices: 1.0
   ChimeraX-PickBlobs: 1.0.1
   ChimeraX-Positions: 1.0
   ChimeraX-PresetMgr: 1.1.2
   ChimeraX-PubChem: 2.2
   ChimeraX-ReadPbonds: 1.0.1
   ChimeraX-Registration: 1.1.2
   ChimeraX-RemoteControl: 1.0
   ChimeraX-RenderByAttr: 1.6.2
   ChimeraX-RenumberResidues: 1.1
   ChimeraX-ResidueFit: 1.0.1
   ChimeraX-RestServer: 1.3.1
   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-Segmentations: 3.5.6
   ChimeraX-SelInspector: 1.0
   ChimeraX-SeqView: 2.14
   ChimeraX-Shape: 1.0.1
   ChimeraX-Shell: 1.0.1
   ChimeraX-Shortcuts: 1.2.0
   ChimeraX-ShowSequences: 1.0.3
   ChimeraX-SideView: 1.0.1
   ChimeraX-SimilarStructures: 1.0.1
   ChimeraX-Smiles: 2.1.2
   ChimeraX-SmoothLines: 1.0
   ChimeraX-SpaceNavigator: 1.0
   ChimeraX-StdCommands: 1.18.1
   ChimeraX-STL: 1.0.1
   ChimeraX-Storm: 1.0
   ChimeraX-StructMeasure: 1.2.1
   ChimeraX-Struts: 1.0.1
   ChimeraX-Surface: 1.0.1
   ChimeraX-SwapAA: 2.0.1
   ChimeraX-SwapRes: 2.5
   ChimeraX-TapeMeasure: 1.0
   ChimeraX-TaskManager: 1.0
   ChimeraX-Test: 1.0
   ChimeraX-Toolbar: 1.2.3
   ChimeraX-ToolshedUtils: 1.2.4
   ChimeraX-Topography: 1.0
   ChimeraX-ToQuest: 1.0
   ChimeraX-Tug: 1.0.1
   ChimeraX-UI: 1.41
   ChimeraX-Umap: 1.0
   ChimeraX-uniprot: 2.3.1
   ChimeraX-UnitCell: 1.0.1
   ChimeraX-ViewDockX: 1.4.4
   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: 1.1.4
   ChimeraX-Zone: 1.0.1
   colorama: 0.4.6
   comm: 0.2.2
   contourpy: 1.3.1
   cxservices: 1.2.3
   cycler: 0.12.1
   Cython: 3.0.10
   debugpy: 1.8.9
   decorator: 5.1.1
   docutils: 0.21.2
   executing: 2.1.0
   filelock: 3.15.4
   fonttools: 4.55.3
   funcparserlib: 2.0.0a0
   glfw: 2.8.0
   grako: 3.16.5
   h11: 0.14.0
   h5py: 3.12.1
   html2text: 2024.2.26
   httpcore: 1.0.7
   httpx: 0.28.1
   idna: 3.10
   ihm: 1.3
   imagecodecs: 2024.6.1
   imagesize: 1.4.1
   ipykernel: 6.29.5
   ipython: 8.26.0
   ipywidgets: 8.1.5
   jedi: 0.19.1
   Jinja2: 3.1.4
   jupyter_client: 8.6.2
   jupyter_core: 5.7.2
   jupyterlab_widgets: 3.0.13
   kiwisolver: 1.4.7
   line_profiler: 4.1.3
   lxml: 5.2.2
   lz4: 4.3.3
   MarkupSafe: 3.0.2
   matplotlib: 3.9.2
   matplotlib-inline: 0.1.7
   msgpack: 1.0.8
   ndindex: 1.9.2
   nest-asyncio: 1.6.0
   netCDF4: 1.6.5
   networkx: 3.3
   nibabel: 5.2.0
   nptyping: 2.5.0
   numexpr: 2.10.2
   numpy: 1.26.4
   openvr: 1.26.701
   packaging: 23.2
   ParmEd: 4.2.2
   parso: 0.8.4
   pep517: 0.13.1
   pexpect: 4.9.0
   pillow: 10.4.0
   pip: 24.2
   pkginfo: 1.11.1
   platformdirs: 4.3.6
   prompt_toolkit: 3.0.48
   psutil: 6.0.0
   ptyprocess: 0.7.0
   pure_eval: 0.2.3
   py-cpuinfo: 9.0.0
   pycollada: 0.8
   pydicom: 2.4.4
   pyelftools: 0.31
   Pygments: 2.18.0
   pynmrstar: 3.3.4
   pynrrd: 1.0.0
   PyOpenGL: 3.1.7
   PyOpenGL-accelerate: 3.1.7
   pyopenxr: 1.0.3401
   pyparsing: 3.2.0
   pyproject_hooks: 1.2.0
   PyQt6-commercial: 6.7.1
   PyQt6-Qt6: 6.7.3
   PyQt6-WebEngine-commercial: 6.7.0
   PyQt6-WebEngine-Qt6: 6.7.3
   PyQt6-WebEngineSubwheel-Qt6: 6.7.3
   PyQt6_sip: 13.8.0
   python-dateutil: 2.9.0.post0
   pytz: 2024.2
   pyzmq: 26.2.0
   qtconsole: 5.5.2
   QtPy: 2.4.2
   qtshim: 1.0
   RandomWords: 0.4.0
   requests: 2.32.3
   scipy: 1.14.0
   setuptools: 72.1.0
   sfftk-rw: 0.8.1
   six: 1.16.0
   sniffio: 1.3.1
   snowballstemmer: 2.2.0
   sortedcontainers: 2.4.0
   soupsieve: 2.6
   Sphinx: 8.0.2
   sphinx-autodoc-typehints: 2.2.3
   sphinxcontrib-applehelp: 2.0.0
   sphinxcontrib-blockdiag: 3.0.0
   sphinxcontrib-devhelp: 2.0.0
   sphinxcontrib-htmlhelp: 2.1.0
   sphinxcontrib-jsmath: 1.0.1
   sphinxcontrib-qthelp: 2.0.0
   sphinxcontrib-serializinghtml: 2.0.0
   stack-data: 0.6.3
   superqt: 0.6.3
   tables: 3.10.1
   tcia_utils: 1.5.1
   tifffile: 2024.7.24
   tinyarray: 1.2.4
   tornado: 6.4.2
   traitlets: 5.14.3
   typing_extensions: 4.12.2
   tzdata: 2024.2
   urllib3: 2.2.3
   wcwidth: 0.2.13
   webcolors: 24.6.0
   wheel: 0.43.0
   wheel-filename: 1.4.1
   widgetsnbextension: 4.0.13
#20135 duplicate Crash on Mac waking from sleep Tom Goddard taic@…
Description 
The following bug report has been submitted:
Platform:        macOS-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x000000031e473000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031d467000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031c45b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031b44f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031a443000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000319437000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031842b000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000031741f000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000316413000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000315407000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003143fb000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003133ef000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000003123e3000 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001f088a0c0 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, lxml._elementpath, lxml.etree, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast (total: 62)


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{
  "uptime" : 2800000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 1816534185,
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  "modelCode" : "MacBookPro18,3",
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  "captureTime" : "2026-04-03 18:27:59.3865 -0400",
  "codeSigningMonitor" : 1,
  "incident" : "9F2F327E-7A28-45FF-A622-C2AE24F97A58",
  "pid" : 61659,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2026-03-17 15:49:30.4754 -0400",
  "procStartAbsTime" : 60473543095781,
  "procExitAbsTime" : 68091359552862,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"0C2BB12E-24B4-5BE2-9EF3-072FD0ADFDC2","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "FA6EEC6E-A890-96AC-901B-4A3BA4995AFD",
  "appleIntelligenceStatus" : {"state":"unavailable","reasons":["notOptedIn","siriAssetIsNotReady","assetIsNotReady"]},
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "codeSigningAuxiliaryInfo" : 0,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "bootSessionUUID" : "52F873D9-CF35-4D9E-BD7E-324140C9F0A7",
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  "vmRegionInfo" : "0x5d790b31a318 is not in any region.  Bytes after previous region: 102293423891225  Bytes before following region: 2778656038120\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      commpage (reserved)        1000000000-7000000000   [384.0G] ---\/--- SM=NUL  reserved VM address space (unallocated)\n--->  GAP OF 0x5f9000000000 BYTES\n      MALLOC_NANO              600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV  ",
  "exception" : {"codes":"0x0000000000000001, 0x00005d790b31a318","rawCodes":[1,102774460228376],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00005d790b31a318"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":61659},
  "ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
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===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_0.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  
Computing secondary structure  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_1.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_2.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_3.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_avavneefl_h_2kb/fold_tcr_avavneefl_h_2kb_model_4.cif

Chain information for fold_tcr_avavneefl_h_2kb_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_0.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_0.cif #6  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_1.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_1.cif #7  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_2.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_2.cif #8  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_3.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_3.cif #9  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2db/fold_tcr_iskanvdvl_h2db_model_4.cif

Chain information for fold_tcr_iskanvdvl_h2db_model_4.cif #10  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_0.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_0.cif #11  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_1.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_1.cif #12  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_2.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_2.cif #13  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_3.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_3.cif #14  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/fold_tcr_iskanvdvl_h2kb/fold_tcr_iskanvdvl_h2kb_model_4.cif

Chain information for fold_tcr_iskanvdvl_h2kb_model_4.cif #15  
---  
Chain | Description  
A | .  
B | .  
C | .  
D | .  
  
Computing secondary structure  

> ui tool show Matchmaker

> matchmaker #2-15 to #1

Computing secondary structure  
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 fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_1.cif, chain D (#2), sequence alignment score =
1469.5  
RMSD between 112 pruned atom pairs is 0.263 angstroms; (across all 274 pairs:
20.703)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_2.cif, chain D (#3), sequence alignment score =
1469.5  
RMSD between 158 pruned atom pairs is 0.262 angstroms; (across all 274 pairs:
18.950)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_3.cif, chain D (#4), sequence alignment score =
1460.5  
RMSD between 152 pruned atom pairs is 0.237 angstroms; (across all 274 pairs:
20.473)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_avavneefl_h_2kb_model_4.cif, chain D (#5), sequence alignment score =
1451.5  
RMSD between 141 pruned atom pairs is 0.178 angstroms; (across all 274 pairs:
19.690)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_0.cif, chain D (#6), sequence alignment score =
1288.3  
RMSD between 177 pruned atom pairs is 0.529 angstroms; (across all 274 pairs:
12.666)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_1.cif, chain D (#7), sequence alignment score =
1297.3  
RMSD between 176 pruned atom pairs is 0.520 angstroms; (across all 274 pairs:
10.517)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_2.cif, chain D (#8), sequence alignment score =
1295.5  
RMSD between 178 pruned atom pairs is 0.578 angstroms; (across all 274 pairs:
10.087)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_3.cif, chain D (#9), sequence alignment score =
1300.9  
RMSD between 177 pruned atom pairs is 0.531 angstroms; (across all 274 pairs:
10.467)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2db_model_4.cif, chain D (#10), sequence alignment score =
1284.7  
RMSD between 176 pruned atom pairs is 0.531 angstroms; (across all 274 pairs:
13.215)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_0.cif, chain D (#11), sequence alignment score =
1449.7  
RMSD between 179 pruned atom pairs is 0.451 angstroms; (across all 274 pairs:
7.791)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_1.cif, chain D (#12), sequence alignment score =
1453.3  
RMSD between 179 pruned atom pairs is 0.374 angstroms; (across all 274 pairs:
10.016)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_2.cif, chain D (#13), sequence alignment score =
1464.1  
RMSD between 181 pruned atom pairs is 0.296 angstroms; (across all 274 pairs:
8.969)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_3.cif, chain D (#14), sequence alignment score =
1471.3  
RMSD between 172 pruned atom pairs is 0.272 angstroms; (across all 274 pairs:
15.272)  
  
Matchmaker fold_tcr_avavneefl_h_2kb_model_0.cif, chain D (#1) with
fold_tcr_iskanvdvl_h2kb_model_4.cif, chain D (#15), sequence alignment score =
1458.7  
RMSD between 165 pruned atom pairs is 0.463 angstroms; (across all 274 pairs:
19.186)  
  

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> color #1 bychain

> show #2 models

> show #3 models

> show #4 models

> show #5 models

> hide #5 models

> hide #4 models

> hide #3 models

> hide #2 models

> show #2 models

> show #3 models

> show #4 models

> show #5 models

> hide #1 models

> delete atoms #2-5

> delete bonds #2-5

> show #1 models

> hide #1 models

> show #6 models

> show #7 models

> show #8 models

> show #9 models

> show #10 models

> ui tool show "Color Actions"

> set bgColor white

> hide #7 models

> hide #8 models

> show #8 models

> show #7 models

> show #6-10 surfaces

> select /C

740 atoms, 730 bonds, 99 residues, 11 models selected  

> hide sel & #!6-10 surfaces

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> hide sel & #!6 surfaces

> select clear

> hide #!6 surfaces

> show #!7 models

> show #!8 models

> show #!9 models

> show #!10 models

> hide #!6-10 surfaces

> select /D

24787 atoms, 25498 bonds, 3034 residues, 11 models selected  

> show sel & #!6-10 surfaces

> hide #!7 models

> hide #!8 models

> hide #!9 models

> hide #!10 models

> show #!7 models

> hide #!6 models

> show #!8 models

> hide #!7 models

> show #!10 models

> hide #!8 models

> show #11 models

> hide #!10 models

> hide #11 models

> show #!6 models

> show #!7 models

> hide #!6 models

> show #!6 models

> show #!8 models

> show #!9 models

> show #!10 models

> hide sel & #!6-10 surfaces

> hide #!6 models

> delete atoms (#!7-10 & sel)

> delete bonds (#!7-10 & sel)

> undo

> select clear

> hide #!6 models

> undo

> hide #!6 models

> delete atoms #7-10

> delete bonds #7-10

> show #!6 models

> show #11 models

> hide #!6 models

> show #12 models

> show #13 models

> show #14 models

> show #15 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> show #11 models

> hide #15 models

> show #15 models

> hide #11 models

> show #11 models

> show #12 models

> hide #15 models

> show #13 models

> hide #12 models

> show #12 models

> hide #11 models

> show #14 models

> hide #12 models

> hide #13 models

> hide #14 models

> show #!6 models

> show #11 models

> show #12 models

> hide #!6 models

> hide #11 models

> hide #12 models

> show #11 models

> color #11 bychain

> show #15 models

> hide #11 models

> color #15 bychain

> show #!6 models

> hide #15 models

> color #!6 bychain

> show #1 models

> hide #1 models

> show #11 models

> hide #!6 models

> show #12 models

> show #13 models

> show #14 models

> show #15 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> show #!6 models

> ui tool show "Show Sequence Viewer"

> sequence chain #6/A

Alignment identifier is 6/A  

> sequence chain #6/B

Alignment identifier is 6/B  

> select
> #6/A:4-7,10-14,19-25,32-37,43-48,52-56,59-64,69-74,83-90,97-99,103-108

501 atoms, 502 bonds, 62 residues, 1 model selected  

> select #6/A:87

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #6/A:87-99

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

> ui tool show "Color Actions"

> set bgColor indian red

> set bgColor white

> color sel brown target acsp

> color sel crimson target acsp

> color sel dark red target acsp

> select #6/B:5-7,10-14,19-24,31-37,44-50,53-56,65-67,73-78,87-94,106-111

465 atoms, 466 bonds, 55 residues, 1 model selected  

> select #6/B:91

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #6/B:91-102

92 atoms, 93 bonds, 12 residues, 1 model selected  

> select #6/B:91

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #6/B:91-102

92 atoms, 93 bonds, 12 residues, 1 model selected  

> color sel maroon target acsp

> select #6/A:87

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #6/A:87-99

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

> color sel medium slate blue target acsp

> color sel indigo target acsp

> color sel medium blue target acsp

> select clear

> select /A:87-:99

Expected an objects specifier or a keyword  

> select /A:87-99

693 atoms, 700 bonds, 91 residues, 7 models selected  

> show #11 models

> show #12 models

> show #13 models

> show #14 models

> show #15 models

> show #1 models

> color sel medium blue target acsp

> select /B:91-102

644 atoms, 651 bonds, 84 residues, 7 models selected  

> color sel maroon target acsp

> hide #!6 models

> hide #11 models

> hide #12 models

> hide #13 models

> hide #14 models

> hide #15 models

> show #!6 models

> hide #1 models

> show #11 models

> hide #!6 models

> show #12 models

> hide #11 models

> show #13 models

> hide #12 models

> show #14 models

> hide #13 models

> show #15 models

> hide #14 models

> show #!6 models

> hide #15 models

> show #15 models

> hide #15 models

> hide #!6 models

> show #12 models

> show #13 models

> show #14 models

> delete atoms (#12-14 & sel)

> delete bonds (#12-14 & sel)

> select clear

> undo

> show #11 models

> hide #!12 models

> hide #!13 models

> show #15 models

> hide #!14 models

> hide #15 models

> select clear

> show #!12 models

> hide #11 models

> show #!13 models

> show #!14 models

> delete atoms #12-14

> delete bonds #12-14

> show #!6 models

> show #11 models

> hide #!6 models

> show #!6 models

> hide #11 models

> show #11 models

> hide #!6 models

> show #15 models

> hide #11 models

> show #11 models

> hide #15 models

> show #15 models

> hide #11 models

> show #!6 models

> hide #15 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/AF3/TCR-
> peptide.cxs

opened ChimeraX session  

> close session

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Hfq_Vcholeria/AF3/HqbA_Hfq_V.cholera.contacts.cxs

opened ChimeraX session  

> hide #3 models

> hide #6 models

> show #6 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #3 models

> select #6/A:5,15

15 atoms, 13 bonds, 2 residues, 1 model selected  

> select #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95

109 atoms, 98 bonds, 13 residues, 1 model selected  

> color sel magenta target acsp

> color sel violet target acsp

> color sel magenta target acsp

> color sel light steel blue target acsp

> color sel sky blue target acsp

> color sel cyan target acsp

> color sel magenta target acsp

> select clear

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel magenta target acsp

> select clear

> show #3,6 surfaces

> hide #!3 models

> show #!3 models

> hide #!3,6 surfaces

> show #!1 models

> hide #!1 models

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select clear

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> show sel atoms

> select clear

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> show sel surfaces

> select #6/A:73

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel surfaces

> select clear

> transparency #3,6 70

> transparency #3,6 40

Drag select of 1 residues  

> hide sel surfaces

> select clear

> hide #!3,6 surfaces

> show #!3,6 surfaces

> hide #!3,6 surfaces

> select #6/C:31

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show sel surfaces

> hide sel surfaces

> color (#!6 & sel) blue

> show sel surfaces

> select clear

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> show sel surfaces

> select clear

> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/E.coli.HqbAmutatnt_Hfq_CoA.png"
> width 900 height 668 supersample 4 transparentBackground true

> select #6/G:49@OG1

1 atom, 1 residue, 1 model selected  
Drag select of fold_hqba_hfqx6_co_model_0.cif_B SES surface, 234 of 122862
triangles  

> select #6/A:5

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #6/A:98

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #6/A:102

24 atoms, 21 bonds, 3 residues, 2 models selected  

> select add #6/A:103

35 atoms, 32 bonds, 4 residues, 2 models selected  

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> show sel surfaces

> hide #!3 models

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> show sel surfaces

> select clear

> hide #!6 surfaces

> show #!3 models

> select #6/A:15,19,23,24,27,41,49,52,67,95,117,126,152,164,167

133 atoms, 122 bonds, 15 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel pale violet red target acsp

> select clear

> select #6/A:15,19,23,24,27,41,49,52,67,95,117,126,152,164,167

133 atoms, 122 bonds, 15 residues, 1 model selected  

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> show sel surfaces

> select clear

> select
> #6/A:5,15,19,23,24,27,36,41,49,52,67,68,95,98,102,103,105,117,126,152,164,167

197 atoms, 183 bonds, 22 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> select clear

> select #6/A:41

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color (#!6 & sel) magenta

> select up

38 atoms, 38 bonds, 5 residues, 2 models selected  

> select up

1311 atoms, 1341 bonds, 167 residues, 2 models selected  

> show sel surfaces

> select clear

> hide #!3,6 surfaces

> undo

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> select ~sel & ##selected

4717 atoms, 4800 bonds, 613 residues, 1 model selected  

> show sel surfaces

> select clear

> save "/Users/taic/OneDrive - National Institutes of
> Health/MacBookPro021/project/SusanG/HqbA_Ni/AF3/E.coli.HqbAmutatnt_Hfq_CoA.2.png"
> width 900 height 668 supersample 4 transparentBackground true

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_0.cif

Chain information for fold_hqba_yhbp_co_model_0.cif #4  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif

Chain information for fold_hqba_yhbp_co_model_1.cif #5  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_2.cif

Chain information for fold_hqba_yhbp_co_model_2.cif #7  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_3.cif

Chain information for fold_hqba_yhbp_co_model_3.cif #8  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_4.cif

Chain information for fold_hqba_yhbp_co_model_4.cif #9  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> hide #4-5,7-9#!3,6 surfaces

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #4-5,7-9 to #6 & sel

Computing secondary structure  
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_0.cif, chain A (#4), sequence alignment score = 852.8  
RMSD between 167 pruned atom pairs is 0.391 angstroms; (across all 167 pairs:
0.391)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_2.cif, chain A (#7), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.278 angstroms; (across all 167 pairs:
0.278)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_3.cif, chain A (#8), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.296 angstroms; (across all 167 pairs:
0.296)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_4.cif, chain A (#9), sequence alignment score = 873.8  
RMSD between 167 pruned atom pairs is 0.297 angstroms; (across all 167 pairs:
0.297)  
  

> hide #!3 models

> show #!3 models

> hide #4 models

> show #4 models

> hide #!6 models

> hide #5 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #!3 models

> show #!6 models

> show #7 models

> hide #!6 models

> show #5 models

> show #8 models

> show #9 models

> color #4-5,7-9 bychain

> select clear

> hide #5 models

> hide #7 models

> show #5 models

> hide #9 models

> hide #8 models

> show #8 models

> hide #5 models

> hide #4 models

> show #5 models

> show #7 models

> delete atoms #5,7-8

> delete bonds #5,7-8

> show #4 models

> show #9 models

> hide #9 models

> show #9 models

> hide #4 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbp_co/fold_hqba_yhbp_co_model_1.cif

Chain information for fold_hqba_yhbp_co_model_1.cif #5  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> color #5,9 bychain

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #5 to #6 & sel

Computing secondary structure  
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)  
  

> hide #9 models

> show #4 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_0.cif

Chain information for fold_hqba_yhbq_co_model_0.cif #7  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_1.cif

Chain information for fold_hqba_yhbq_co_model_1.cif #8  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_2.cif

Chain information for fold_hqba_yhbq_co_model_2.cif #10  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_3.cif

Chain information for fold_hqba_yhbq_co_model_3.cif #11  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq_co/fold_hqba_yhbq_co_model_4.cif

Chain information for fold_hqba_yhbq_co_model_4.cif #12  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #4-5,7-12 to #6 & sel

Computing secondary structure  
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_0.cif, chain A (#4), sequence alignment score = 852.8  
RMSD between 167 pruned atom pairs is 0.391 angstroms; (across all 167 pairs:
0.391)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_1.cif, chain A (#5), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.433 angstroms; (across all 167 pairs:
0.433)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_0.cif, chain A (#7), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.202 angstroms; (across all 167 pairs:
0.202)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_1.cif, chain A (#8), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.376 angstroms; (across all 167 pairs:
0.376)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbp_co_model_4.cif, chain A (#9), sequence alignment score = 873.8  
RMSD between 167 pruned atom pairs is 0.297 angstroms; (across all 167 pairs:
0.297)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
0.280)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
0.317)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
0.293)  
  

> hide #4 models

> hide #5 models

> hide #8 models

> hide #10 models

> hide #11 models

> hide #12 models

> show #8 models

> hide #7 models

> show #10 models

> hide #8 models

> show #11 models

> hide #10 models

> show #12 models

> hide #11 models

> show #4 models

> hide #4 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> show #!3 models

> hide #12 models

> show #12 models

> hide #!3 models

> show #!3 models

> hide #!6 models

> show #!6 models

> hide #12 models

> select clear

> show #7 models

> hide #7 models

> show #4 models

> hide #!6 models

> hide #4 models

> show #!6 models

> hide #!6 models

> show #4 models

> show #5 models

> hide #5 models

> show #5 models

> hide #4 models

> hide #5 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #7 models

> color #7#!3 bychain

> hide #7 models

> color #3 lime

> show #7 models

> show #8 models

> hide #7 models

> show #7 models

> hide #8 models

> show #9 models

> hide #9 models

> show #10 models

> hide #10 models

> show #11 models

> hide #11 models

> show #12 models

> hide #12 models

> show #9 models

> hide #!3 models

> hide #7 models

> show #5 models

> hide #9 models

> show #9 models

> hide #5 models

> delete atoms #9

> delete bonds #9

> show #7 models

> show #!3 models

> show #8 models

> hide #7 models

> show #7 models

> hide #8 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #8 models

> show #10 models

> show #11 models

> show #12 models

> hide #7 models

> hide #!3 models

> show #4 models

> hide #8 models

> hide #10 models

> hide #12 models

> hide #11 models

> show #!6 models

> show #5 models

> hide #4 models

> hide #!6 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_0.cif

Chain information for fold_hqba_ubiu_model_0.cif #9  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_1.cif

Chain information for fold_hqba_ubiu_model_1.cif #13  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_2.cif

Chain information for fold_hqba_ubiu_model_2.cif #14  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_3.cif

Chain information for fold_hqba_ubiu_model_3.cif #15  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_ubiu/fold_hqba_ubiu_model_4.cif

Chain information for fold_hqba_ubiu_model_4.cif #16  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> show #!6 models

> hide #5 models

> hide #9 models

> ui tool show Matchmaker

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #9-16 to #6 & sel

Computing secondary structure  
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
0.273)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
0.280)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
0.317)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
0.293)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_1.cif, chain A (#13), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.260 angstroms; (across all 167 pairs:
0.260)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_2.cif, chain A (#14), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.235 angstroms; (across all 167 pairs:
0.235)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_3.cif, chain A (#15), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.229 angstroms; (across all 167 pairs:
0.229)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_4.cif, chain A (#16), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.219 angstroms; (across all 167 pairs:
0.219)  
  

> show #9 models

> hide #!6 models

> show #!6 models

> hide #9 models

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> hide #13 models

> hide #14 models

> hide #15 models

> hide #16 models

> show #9 models

> hide #!6 models

> ui tool show Matchmaker

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> matchmaker #9-16 to #6 & sel

Computing secondary structure  
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_0.cif, chain A (#9), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.273 angstroms; (across all 167 pairs:
0.273)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_2.cif, chain A (#10), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.280 angstroms; (across all 167 pairs:
0.280)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_3.cif, chain A (#11), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.317 angstroms; (across all 167 pairs:
0.317)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_co_model_4.cif, chain A (#12), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.293 angstroms; (across all 167 pairs:
0.293)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_1.cif, chain A (#13), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.260 angstroms; (across all 167 pairs:
0.260)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_2.cif, chain A (#14), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.235 angstroms; (across all 167 pairs:
0.235)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_3.cif, chain A (#15), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.229 angstroms; (across all 167 pairs:
0.229)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_ubiu_model_4.cif, chain A (#16), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.219 angstroms; (across all 167 pairs:
0.219)  
  

> show #!6 models

> hide #!6 models

> show #13 models

> show #14 models

> show #15 models

> show #16 models

> hide #9 models

> delete atoms #13-16

> delete bonds #13-16

> show #9 models

> color #9 bychain

> show #!6 models

> show #!3 models

> hide #!6 models

> show #!6 models

> hide #9 models

> select clear

> select #6/A:164

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #6/A:23,24,27

24 atoms, 22 bonds, 3 residues, 1 model selected  

> select #6/A:23,24,27,167

36 atoms, 34 bonds, 4 residues, 1 model selected  

> color (#!6 & sel) cyan

> select clear

> show #9 models

> hide #!6 models

> show #7 models

> hide #9 models

> show #!6 models

> hide #!6 models

> show #8 models

> show #10 models

> show #11 models

> show #12 models

> hide #8 models

> hide #10 models

> hide #11 models

> hide #12 models

> show #!6 models

> hide #7 models

> show #4 models

> show #5 models

> hide #!6 models

> hide #5 models

> show #5 models

> hide #4 models

> show #!6 models

> hide #5 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_0.cif

Chain information for fold_hqba_yhbq_model_0.cif #13  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_1.cif

Chain information for fold_hqba_yhbq_model_1.cif #14  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_2.cif

Chain information for fold_hqba_yhbq_model_2.cif #15  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_3.cif

Chain information for fold_hqba_yhbq_model_3.cif #16  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/SusanG/HqbA_Ni/AF3/fold_hqba_yhbq/fold_hqba_yhbq_model_4.cif

Chain information for fold_hqba_yhbq_model_4.cif #17  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> select #6/A

1311 atoms, 1341 bonds, 167 residues, 1 model selected  

> ui tool show Matchmaker

> matchmaker #13-17 to #6 & sel

Computing secondary structure  
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
0.328)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_1.cif, chain A (#14), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.165 angstroms; (across all 167 pairs:
0.165)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_2.cif, chain A (#15), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.359 angstroms; (across all 167 pairs:
0.359)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_3.cif, chain A (#16), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.208 angstroms; (across all 167 pairs:
0.208)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_4.cif, chain A (#17), sequence alignment score = 873.8  
RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
0.288)  
  

> matchmaker #13-17 to #6 & sel

Computing secondary structure  
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 fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_0.cif, chain A (#13), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.328 angstroms; (across all 167 pairs:
0.328)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_1.cif, chain A (#14), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.165 angstroms; (across all 167 pairs:
0.165)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_2.cif, chain A (#15), sequence alignment score = 867.8  
RMSD between 167 pruned atom pairs is 0.359 angstroms; (across all 167 pairs:
0.359)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_3.cif, chain A (#16), sequence alignment score = 870.8  
RMSD between 167 pruned atom pairs is 0.208 angstroms; (across all 167 pairs:
0.208)  
  
Matchmaker fold_hqba_hfqx6_co_model_0.cif, chain A (#6) with
fold_hqba_yhbq_model_4.cif, chain A (#17), sequence alignment score = 873.8  
RMSD between 167 pruned atom pairs is 0.288 angstroms; (across all 167 pairs:
0.288)  
  

> hide #!6 models

> show #7 models

> show #8 models

> hide #8 models

> show #8 models

> show #10 models

> show #11 models

> hide #11 models

> show #11 models

> show #12 models

> hide #!3 models

> hide #7 models

> hide #13 models

> delete atoms #8,10-12,14-17

> delete bonds #8,10-12,14-17

> show #4 models

> show #5 models

> hide #5 models

> show #7 models

> show #9 models

> hide #7 models

> hide #4 models

> show #13 models

> show #!6 models

[deleted to fit within ticket limits]


> hide #5 models

> show #1 models

> show #!2 models

> hide #1 models

> show #1 models

> hide #4 models

> show #3 models

> hide #!2 models

> hide #1 models

> show #!6 models

> hide #3#!6 surfaces

> show #7 models

> hide #!6 models

> hide #3 models

> show #8 models

> hide #7 models

> show #9 models

> hide #8 models

> rainbow #9

> show #10 models

> hide #9 models

> show #11 models

> hide #10 models

> show #1 models

> hide #1 models

> show #1 models

> hide #11 models

> show #11 models

> show #12 models

> hide #11 models

> hide #1 models

> matchmaker #8-10,12 to #7/A pairing bs

Computing secondary structure  
[Repeated 4 time(s)]  Parameters  
---  
Chain pairing | bs  
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 fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56  
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)  
  
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5  
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)  
  
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2  
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)  
  
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_suca_model_0.cif,
chain A (#12), sequence alignment score = 124  
RMSD between 16 pruned atom pairs is 1.040 angstroms; (across all 346 pairs:
29.841)  
  

> show #7 models

> hide #12 models

> show #8 models

> show #9 models

> hide #8 models

> hide #7 models

> show #8 models

> hide #9 models

> show #12 models

> hide #8 models

> rainbow #12

> show #7 models

> hide #12 models

> show #8 models

> hide #7 models

> show #5 models

> hide #8 models

> color #5 bychain

> show #!6 models

> hide #5 models

> show #11 models

> hide #!6 models

> show #!2 models

> hide #!2 models

> show #5 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #5 models

> select /A

32114 atoms, 32801 bonds, 4077 residues, 12 models selected  

> ui tool show Matchmaker

> matchmaker #3-5,7-12#!2,6 & sel to #1/A & sel pairing bs

Computing secondary structure  
[Repeated 6 time(s)]  Parameters  
---  
Chain pairing | bs  
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 fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.324 angstroms; (across all 208 pairs:
0.324)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1074.2  
RMSD between 208 pruned atom pairs is 0.403 angstroms; (across all 208 pairs:
0.403)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_fad_model_0.cif, chain A (#3), sequence alignment score =
1077.8  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1083.8  
RMSD between 208 pruned atom pairs is 0.351 angstroms; (across all 208 pairs:
0.351)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1083.2  
RMSD between 208 pruned atom pairs is 0.359 angstroms; (across all 208 pairs:
0.359)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 86.4  
RMSD between 6 pruned atom pairs is 1.359 angstroms; (across all 168 pairs:
21.278)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 62.8  
RMSD between 4 pruned atom pairs is 1.139 angstroms; (across all 65 pairs:
22.621)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 62.2  
RMSD between 25 pruned atom pairs is 1.174 angstroms; (across all 153 pairs:
31.595)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 62.4  
RMSD between 7 pruned atom pairs is 1.252 angstroms; (across all 189 pairs:
25.278)  
  
Matchmaker fold_azor_monomer_model_0.cif, chain A (#1) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2  
RMSD between 5 pruned atom pairs is 1.071 angstroms; (across all 101 pairs:
17.409)  
  

> show #1 models

> hide #1 models

> show #5 models

> hide #11 models

> show #11 models

> hide #5 models

> select ::name="NAD"

88 atoms, 96 bonds, 2 residues, 2 models selected  

> select ~sel & ##selected

4938 atoms, 5055 bonds, 624 residues, 2 models selected  

> rainbow sel & #11

> select clear

> show #1 models

> hide #11 models

> open 9H2I fromDatabase pdb format mmcif

Summary of feedback from opening 9H2I fetched from pdb  
---  
note | Fetching compressed mmCIF 9h2i from http://files.rcsb.org/download/9h2i.cif  
  
9h2i title:  
Dihydrolipoyl Dehydrogenase (E3) in complex with the binding domain of
Dihydrolipoamide Acetyltransferase (E2) from the E. coli pyruvate
dehydrogenase complex [more info...]  
  
Chain information for 9h2i #13  
---  
Chain | Description | UniProt  
A | Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex | ODP2_ECOLI 314-379  
B C | Dihydrolipoyl dehydrogenase | DLDH_ECOLI 2-474  
  
Non-standard residues in 9h2i #13  
---  
FAD — flavin-adenine dinucleotide  
  

> ui tool show Matchmaker

> matchmaker #13 to #1/A pairing bs

Computing secondary structure  
Parameters  
---  
Chain pairing | bs  
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 fold_azor_monomer_model_0.cif, chain A (#1) with 9h2i, chain B
(#13), sequence alignment score = 64.3  
RMSD between 6 pruned atom pairs is 0.906 angstroms; (across all 61 pairs:
18.939)  
  

> undo

> select ::name="NAD"

88 atoms, 96 bonds, 2 residues, 2 models selected  

> hide #11 models

> hide #1 models

> show #4 models

> hide #13 models

> select ::name="FAD"

265 atoms, 290 bonds, 5 residues, 4 models selected  

> show #13 models

> hide #4 models

> color sel & #13 bychain

> undo

> select clear

> color #13 bychain

> undo

> select ::name="FAD"

265 atoms, 290 bonds, 5 residues, 4 models selected  

> matchmaker #13 & sel to #4/A & sel pairing bs

No 'to' chains specified  

> matchmaker #13 & sel to #4/A & sel pairing bs

No 'to' chains specified  

> matchmaker #13 & sel to #6 & sel

No matrix compatible with both reference structure and all match structures  

> select clear

> select ::name="FAD"

265 atoms, 290 bonds, 5 residues, 4 models selected  

> matchmaker #13 to #6 & sel

No matrix compatible with both reference structure and all match structures  

> matchmaker #13 to #6

Computing secondary structure  
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 fold_azor_monomer_fad_model_0.cif, chain A (#6) with 9h2i, chain B
(#13), sequence alignment score = 64.3  
RMSD between 6 pruned atom pairs is 0.976 angstroms; (across all 61 pairs:
18.887)  
  

> show #!6 models

> hide #13 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> open 8RX4 fromDatabase pdb format mmcif

Summary of feedback from opening 8RX4 fetched from pdb  
---  
notes | Fetching compressed mmCIF 8rx4 from http://files.rcsb.org/download/8rx4.cif  
Fetching CCD NAP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NAP/NAP.cif  
  
8rx4 title:  
Mycothione reductase from Mycobacterium xenopi in complex with co-factor FAD
and redox co-factor NADP(H) [more info...]  
  
Chain information for 8rx4 #14  
---  
Chain | Description | UniProt  
A B | Mycothione reductase | X8E6Y0_MYCXE 1-459  
  
Non-standard residues in 8rx4 #14  
---  
FAD — flavin-adenine dinucleotide  
NAP — nadp nicotinamide-adenine-dinucleotide phosphate
(2'-monophosphoadenosine 5'-diphosphoribose)  
  

> hide #!6 models

> matchmaker #14 to #13

Computing secondary structure  
[Repeated 1 time(s)]  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 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3  
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)  
  

> show #13 models

> select ::name="FAD"

371 atoms, 406 bonds, 7 residues, 5 models selected  

> select ~sel & ##selected

21835 atoms, 21626 bonds, 3388 residues, 5 models selected  

> color sel & #13-14 bychain

> select clear

> hide #14 models

> show #14 models

> hide #13 models

> show #13 models

> hide #14 models

> show #14 models

> hide #13 models

> select #14/B

3646 atoms, 3705 bonds, 481 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #13 models

> hide #14 models

> select #13/C

3803 atoms, 3650 bonds, 693 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> hide sel atoms

> select #13/B

3924 atoms, 3668 bonds, 798 residues, 1 model selected  

> rainbow sel

> select clear

> show #4 models

> hide #13 models

> show #14 models

> show #13 models

> hide #14 models

> hide #4 models

> show #!6 models

> hide #13 models

> show #13 models

> select #13/B:429

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #13/B:429

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "move picked models"

> view matrix models
> #13,-0.24553,0.95614,-0.15973,-12.311,-0.87052,-0.14498,0.4703,-33.244,0.42651,0.25452,0.86793,37.123

> select clear

> show #3 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select ::name="FAD"

371 atoms, 406 bonds, 7 residues, 5 models selected  

> hide #13 models

> select ~sel & ##selected

21835 atoms, 21626 bonds, 3388 residues, 5 models selected  

> color sel & #3 bychain

> select clear

> show #13 models

> select #13/B:118

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #13,0.033187,-0.97762,-0.20777,14.167,0.99779,0.020425,0.063272,41.991,-0.057612,-0.20941,0.97613,20.908

> view matrix models
> #13,0.61108,-0.5049,-0.60964,43.097,0.74854,0.11812,0.65248,13.491,-0.25743,-0.85506,0.45012,36.524

Drag select of 1 residues  

> view matrix models
> #13,0.69637,-0.51088,-0.50406,42.577,0.69997,0.32838,0.6342,10.762,-0.15848,-0.79446,0.58627,34.933

> view matrix models
> #13,0.60362,-0.77451,-0.18916,31.241,0.57555,0.25913,0.77562,2.4774,-0.55171,-0.57705,0.60219,19.363

> view matrix models
> #13,0.57452,-0.7742,-0.2656,32.755,0.56401,0.13931,0.81393,1.7918,-0.59314,-0.61742,0.5167,21.081

> view matrix models
> #13,0.50768,-0.80838,-0.29797,31.826,0.63814,0.12046,0.76044,6.2021,-0.57883,-0.57621,0.57701,19.262

> view matrix models
> #13,0.41134,-0.8476,-0.33522,30.098,0.72496,0.081317,0.68397,11.956,-0.55248,-0.52437,0.64793,17.418

> view matrix models
> #13,0.50347,-0.56782,-0.65123,41.319,0.83944,0.14298,0.52431,20.563,-0.2046,-0.81064,0.54863,34.733

> view matrix models
> #13,0.81357,-0.39993,-0.42208,42.973,0.56489,0.37157,0.73677,2.4881,-0.13783,-0.83785,0.52822,37.879

> select clear

> select #13/B:81

7 atoms, 6 bonds, 1 residue, 1 model selected  

> view matrix models
> #13,0.81385,-0.37394,-0.44476,43.517,0.57225,0.38291,0.7252,3.0254,-0.10088,-0.84472,0.52562,39.27

> view matrix models
> #13,0.80931,-0.3118,-0.49779,44.601,0.58724,0.41087,0.69738,4.2194,-0.01291,-0.85672,0.51563,42.67

> view matrix models
> #13,0.83554,-0.52523,-0.16124,36.183,0.53716,0.84258,0.038938,20.618,0.11541,-0.11915,0.98615,25.714

> view matrix models
> #13,0.85682,-0.51537,0.016019,31.023,0.50956,0.85108,0.12652,16.749,-0.07884,-0.10025,0.99183,18.802

> view matrix models
> #13,0.13465,-0.7299,-0.67016,30.752,0.80312,-0.31576,0.50527,23.627,-0.58041,-0.60625,0.54368,20.54

> select clear

[Repeated 1 time(s)]Drag select of 5 residues, 1 bonds  

> show #5 models

> hide #3 models

> show #3 models

> hide #5 models

> show #14 models

> matchmaker #14 to #13

Computing secondary structure  
[Repeated 1 time(s)]  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 9h2i, chain B (#13) with 8rx4, chain A (#14), sequence alignment
score = 815.3  
RMSD between 278 pruned atom pairs is 1.096 angstroms; (across all 447 pairs:
3.176)  
  

> hide #13 models

> show #13 models

> select ::name="FAD"

371 atoms, 406 bonds, 7 residues, 5 models selected  

> select ~sel & ##selected

21835 atoms, 21626 bonds, 3388 residues, 5 models selected  

> show sel & #3,13-14 surfaces

> hide #!14 models

> hide sel & #!3,13 surfaces

> show #!14 models

> hide #!13 models

> hide sel & #!3,14 surfaces

> select clear

> hide #!3 models

> select ::name="NAD"

88 atoms, 96 bonds, 2 residues, 2 models selected  

> select ::name="NAP"

96 atoms, 104 bonds, 2 residues, 1 model selected  

> show #!13 models

> select clear

> hide #!13 models

> show #!13 models

> hide #!13 models

> select ::name="FAD"

371 atoms, 406 bonds, 7 residues, 5 models selected  

> select ~sel & ##selected

21835 atoms, 21626 bonds, 3388 residues, 5 models selected  

> rainbow sel & #!14

> select clear

> select ::name="NAP"

96 atoms, 104 bonds, 2 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(NAP) ``  
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`  
(NAP) ``  
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`  
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAP) ``  
(NAP) ``  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAP) `Info: Total number of electrons: 384; net charge: -3`  
(NAP) ``  
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(NAP) ``  
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`  
(NAP) ``  
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmpzd_topmc/ante.in.mol2);
atoms read (73), bonds read (77).`  
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAP) ``  
(NAP) ``  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAP) `Info: Total number of electrons: 384; net charge: -3`  
(NAP) ``  
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      217
    | QMMM:    diag iterations used for timing =        4
    | QMMM:
    | QMMM:              Internal diag routine = 0.051654 seconds
    | QMMM:                 Dspev diag routine = 0.044332 seconds
    | QMMM:                Dspevd diag routine = 0.032116 seconds
    | QMMM:                Dspevx diag routine = 0.153242 seconds
    | QMMM:                 Dsyev diag routine = 0.047097 seconds
    | QMMM:                Dsyevd diag routine = 0.033935 seconds
    | QMMM:                Dsyevr diag routine = 0.038554 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.022789 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      P       17.4620    0.4650   57.8060
      QMMM:     2        2      O       16.5620   -0.5740   58.3900
      QMMM:     3        3      O       18.0440    0.2210   56.4520
      QMMM:     4        4      O       18.6480    0.7880   58.8450
      QMMM:     5        5      C       18.2700    1.3930   60.1070
      QMMM:     6        6      C       19.4870    1.8540   60.8730
      QMMM:     7        7      O       19.0230    2.6210   62.0160
      QMMM:     8        8      C       20.3910    0.7570   61.4600
      QMMM:     9        9      O       21.7470    1.1830   61.4090
      QMMM:    10       10      C       19.8810    0.6600   62.8920
      QMMM:    11       11      O       20.8230    0.1440   63.8270
      QMMM:    12       12      C       19.6340    2.1310   63.1840
      QMMM:    13       13      N       18.7140    2.3450   64.2950
      QMMM:    14       14      C       17.4200    1.8950   64.3780
      QMMM:    15       15      N       16.8230    2.2310   65.4940
      QMMM:    16       16      C       17.7860    2.9360   66.2020
      QMMM:    17       17      C       17.7680    3.5530   67.4670
      QMMM:    18       18      N       16.7090    3.5600   68.2720
      QMMM:    19       19      N       18.9020    4.1690   67.8780
      QMMM:    20       20      C       19.9640    4.1590   67.0630
      QMMM:    21       21      N       20.0960    3.6140   65.8570
      QMMM:    22       22      C       18.9590    3.0090   65.4750
      QMMM:    23       23      O       16.6940    1.8750   57.8220
      QMMM:    24       24      P       16.8310    3.1760   56.8950
      QMMM:    25       25      O       16.1610    4.3450   57.5500
      QMMM:    26       26      O       18.2590    3.2930   56.4770
      QMMM:    27       27      O       15.9430    2.7150   55.6410
      QMMM:    28       28      C       14.5280    2.4980   55.8770
      QMMM:    29       29      C       13.9670    1.5170   54.8750
      QMMM:    30       30      O       14.0230    2.0920   53.5500
      QMMM:    31       31      C       14.6700    0.1520   54.7880
      QMMM:    32       32      O       13.7350   -0.9120   54.6620
      QMMM:    33       33      C       15.5640    0.2940   53.5490
      QMMM:    34       34      O       15.7840   -0.9330   52.8700
      QMMM:    35       35      C       14.7120    1.2110   52.6690
      QMMM:    36       36      N       15.5520    2.0170   51.7640
      QMMM:    37       37      C       15.9700    1.4830   50.5670
      QMMM:    38       38      C       16.8040    2.2160   49.7300
      QMMM:    39       39      C       17.2170    1.5960   48.4310
      QMMM:    40       40      O       16.7920    0.4660   48.1440
      QMMM:    41       41      N       18.0490    2.2680   47.6420
      QMMM:    42       42      C       17.1960    3.4950   50.0970
      QMMM:    43       43      C       16.7690    4.0240   51.3000
      QMMM:    44       44      C       15.9580    3.2770   52.1340
      QMMM:    45       45      P       20.6860   -1.4490   64.0240
      QMMM:    46       46      O       21.7060   -1.8020   65.0890
      QMMM:    47       47      O       21.0090   -2.0990   62.6800
      QMMM:    48       48      O       19.2630   -1.7280   64.4740
      QMMM:    49       49      H       17.7290    0.6600   60.7060
      QMMM:    50       50      H       17.6220    2.2480   59.9150
      QMMM:    51       51      H       20.0850    2.5010   60.2310
      QMMM:    52       52      H       20.2560   -0.1860   60.9310
      QMMM:    53       53      H       22.3250    0.4250   61.5240
      QMMM:    54       54      H       18.9490    0.0970   62.9320
      QMMM:    55       55      H       20.5770    2.6470   63.3660
      QMMM:    56       56      H       16.9410    1.3200   63.5990
      QMMM:    57       57      H       15.8540    3.1050   67.9850
      QMMM:    58       58      H       16.7600    4.0200   69.1700
      QMMM:    59       59      H       20.8400    4.6670   67.4390
      QMMM:    60       60      H       14.0000    3.4470   55.7840
      QMMM:    61       61      H       14.3870    2.1050   56.8840
      QMMM:    62       62      H       12.9200    1.3420   55.1230
      QMMM:    63       63      H       15.2870   -0.0020   55.6730
      QMMM:    64       64      H       13.8800   -1.5500   55.3640
      QMMM:    65       65      H       16.5100    0.7710   53.8050
      QMMM:    66       66      H       16.3180   -1.5120   53.4190
      QMMM:    67       67      H       13.9980    0.6220   52.0930
      QMMM:    68       68      H       15.6500    0.4930   50.2770
      QMMM:    69       69      H       18.3800    3.1810   47.9180
      QMMM:    70       70      H       18.3500    1.8650   46.7660
      QMMM:    71       71      H       17.8320    4.0750   49.4450
      QMMM:    72       72      H       17.0690    5.0210   51.5890
      QMMM:    73       73      H       15.6420    3.6860   53.0820
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.2168E+07 DeltaE =  -0.4757E+03 DeltaP =   0.9525E+00
    QMMM: Smallest DeltaE =   0.8289E-07 DeltaP =   0.1057E-04 Step =      3
    
    

  
Failure running ANTECHAMBER for residue NAP Check reply log for details  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue NAP (net charge -3) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(NAP) ``  
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`  
(NAP) ``  
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`  
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAP) ``  
(NAP) ``  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAP) `Info: Total number of electrons: 384; net charge: -3`  
(NAP) ``  
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
Charges failed to converge using fast method; re-running using slower more
stable method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2 -fi
mol2 -o
/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.out.mol2 -fo
mol2 -c bcc -nc -3 -j 5 -s 2 -dr n  
(NAP) ``  
(NAP) `Welcome to antechamber 20.0: molecular input file processor.`  
(NAP) ``  
(NAP) `Info: Finished reading file
(/var/folders/dj/31s_fwr51m57z3r5dprv7sh1p4c759/T/tmp25z134no/ante.in.mol2);
atoms read (73), bonds read (77).`  
(NAP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(NAP) ``  
(NAP) ``  
(NAP) `Running:
/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(NAP) `Info: Total number of electrons: 384; net charge: -3`  
(NAP) ``  
(NAP) `Running: /Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O
-i sqm.in -o sqm.out`  
(NAP) `/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/antechamber:
Fatal Error!`  
(NAP) `Cannot properly run
"/Applications/ChimeraX-1.9.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out".`  
  
Contents of sqm.out:

    
    
                --------------------------------------------------------
                                 AMBER SQM VERSION 19
     
                                         By
                  Ross C. Walker, Michael F. Crowley, Scott Brozell,
                             Tim Giese, Andreas W. Goetz,
                            Tai-Sung Lee and David A. Case
     
                --------------------------------------------------------
     
    
    --------------------------------------------------------------------------------
      QM CALCULATION INFO
    --------------------------------------------------------------------------------
    
    | QMMM: Citation for AMBER QMMM Run:
    | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
    
    QMMM: SINGLET STATE CALCULATION
    QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS =132
    
    | QMMM: *** Selected Hamiltonian *** 
    | QMMM: AM1         
    
    | QMMM: *** Parameter sets in use ***
    | QMMM: P : M.J.S.DEWAR et al. THEOCHEM, 187,1, (1989)
    | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985)
    
    | QMMM: *** SCF convergence criteria ***
    | QMMM: Energy change                :  0.1D-09 kcal/mol
    | QMMM: Error matrix |FP-PF|         :  0.1D+00 au
    | QMMM: Density matrix change        :  0.5D-06
    | QMMM: Maximum number of SCF cycles :     1000
    
    | QMMM: *** Diagonalization Routine Information ***
    | QMMM: Pseudo diagonalizations are allowed.
    | QMMM: Auto diagonalization routine selection is in use.
    | QMMM:
    | QMMM: Timing diagonalization routines:
    | QMMM:                              norbs =      217
    | QMMM:    diag iterations used for timing =        4
    | QMMM:
    | QMMM:              Internal diag routine = 0.050281 seconds
    | QMMM:                 Dspev diag routine = 0.043968 seconds
    | QMMM:                Dspevd diag routine = 0.032120 seconds
    | QMMM:                Dspevx diag routine = 0.153124 seconds
    | QMMM:                 Dsyev diag routine = 0.047103 seconds
    | QMMM:                Dsyevd diag routine = 0.033926 seconds
    | QMMM:                Dsyevr diag routine = 0.039887 seconds
    | QMMM:
    | QMMM:                Pseudo diag routine = 0.024004 seconds
    | QMMM:
    | QMMM: Using dspevd routine (diag_routine=3).
    
      QMMM: QM Region Cartesian Coordinates (*=link atom) 
      QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
      QMMM:     1        1      P       17.4620    0.4650   57.8060
      QMMM:     2        2      O       16.5620   -0.5740   58.3900
      QMMM:     3        3      O       18.0440    0.2210   56.4520
      QMMM:     4        4      O       18.6480    0.7880   58.8450
      QMMM:     5        5      C       18.2700    1.3930   60.1070
      QMMM:     6        6      C       19.4870    1.8540   60.8730
      QMMM:     7        7      O       19.0230    2.6210   62.0160
      QMMM:     8        8      C       20.3910    0.7570   61.4600
      QMMM:     9        9      O       21.7470    1.1830   61.4090
      QMMM:    10       10      C       19.8810    0.6600   62.8920
      QMMM:    11       11      O       20.8230    0.1440   63.8270
      QMMM:    12       12      C       19.6340    2.1310   63.1840
      QMMM:    13       13      N       18.7140    2.3450   64.2950
      QMMM:    14       14      C       17.4200    1.8950   64.3780
      QMMM:    15       15      N       16.8230    2.2310   65.4940
      QMMM:    16       16      C       17.7860    2.9360   66.2020
      QMMM:    17       17      C       17.7680    3.5530   67.4670
      QMMM:    18       18      N       16.7090    3.5600   68.2720
      QMMM:    19       19      N       18.9020    4.1690   67.8780
      QMMM:    20       20      C       19.9640    4.1590   67.0630
      QMMM:    21       21      N       20.0960    3.6140   65.8570
      QMMM:    22       22      C       18.9590    3.0090   65.4750
      QMMM:    23       23      O       16.6940    1.8750   57.8220
      QMMM:    24       24      P       16.8310    3.1760   56.8950
      QMMM:    25       25      O       16.1610    4.3450   57.5500
      QMMM:    26       26      O       18.2590    3.2930   56.4770
      QMMM:    27       27      O       15.9430    2.7150   55.6410
      QMMM:    28       28      C       14.5280    2.4980   55.8770
      QMMM:    29       29      C       13.9670    1.5170   54.8750
      QMMM:    30       30      O       14.0230    2.0920   53.5500
      QMMM:    31       31      C       14.6700    0.1520   54.7880
      QMMM:    32       32      O       13.7350   -0.9120   54.6620
      QMMM:    33       33      C       15.5640    0.2940   53.5490
      QMMM:    34       34      O       15.7840   -0.9330   52.8700
      QMMM:    35       35      C       14.7120    1.2110   52.6690
      QMMM:    36       36      N       15.5520    2.0170   51.7640
      QMMM:    37       37      C       15.9700    1.4830   50.5670
      QMMM:    38       38      C       16.8040    2.2160   49.7300
      QMMM:    39       39      C       17.2170    1.5960   48.4310
      QMMM:    40       40      O       16.7920    0.4660   48.1440
      QMMM:    41       41      N       18.0490    2.2680   47.6420
      QMMM:    42       42      C       17.1960    3.4950   50.0970
      QMMM:    43       43      C       16.7690    4.0240   51.3000
      QMMM:    44       44      C       15.9580    3.2770   52.1340
      QMMM:    45       45      P       20.6860   -1.4490   64.0240
      QMMM:    46       46      O       21.7060   -1.8020   65.0890
      QMMM:    47       47      O       21.0090   -2.0990   62.6800
      QMMM:    48       48      O       19.2630   -1.7280   64.4740
      QMMM:    49       49      H       17.7290    0.6600   60.7060
      QMMM:    50       50      H       17.6220    2.2480   59.9150
      QMMM:    51       51      H       20.0850    2.5010   60.2310
      QMMM:    52       52      H       20.2560   -0.1860   60.9310
      QMMM:    53       53      H       22.3250    0.4250   61.5240
      QMMM:    54       54      H       18.9490    0.0970   62.9320
      QMMM:    55       55      H       20.5770    2.6470   63.3660
      QMMM:    56       56      H       16.9410    1.3200   63.5990
      QMMM:    57       57      H       15.8540    3.1050   67.9850
      QMMM:    58       58      H       16.7600    4.0200   69.1700
      QMMM:    59       59      H       20.8400    4.6670   67.4390
      QMMM:    60       60      H       14.0000    3.4470   55.7840
      QMMM:    61       61      H       14.3870    2.1050   56.8840
      QMMM:    62       62      H       12.9200    1.3420   55.1230
      QMMM:    63       63      H       15.2870   -0.0020   55.6730
      QMMM:    64       64      H       13.8800   -1.5500   55.3640
      QMMM:    65       65      H       16.5100    0.7710   53.8050
      QMMM:    66       66      H       16.3180   -1.5120   53.4190
      QMMM:    67       67      H       13.9980    0.6220   52.0930
      QMMM:    68       68      H       15.6500    0.4930   50.2770
      QMMM:    69       69      H       18.3800    3.1810   47.9180
      QMMM:    70       70      H       18.3500    1.8650   46.7660
      QMMM:    71       71      H       17.8320    4.0750   49.4450
      QMMM:    72       72      H       17.0690    5.0210   51.5890
      QMMM:    73       73      H       15.6420    3.6860   53.0820
    
    --------------------------------------------------------------------------------
      RESULTS
    --------------------------------------------------------------------------------
    
    
    QMMM: ERROR!
    QMMM: Unable to achieve self consistency to the tolerances specified
    QMMM: No convergence in SCF after   1000 steps.
    QMMM: E =  -0.2168E+07 DeltaE =  -0.4757E+03 DeltaP =   0.9525E+00
    QMMM: Smallest DeltaE =   0.8289E-07 DeltaP =   0.1057E-04 Step =      3
    
    

  
Failure running ANTECHAMBER for residue NAP Check reply log for details  

> color bfactor sel

96 atoms, 2 residues, atom bfactor range 41.3 to 73.2  

> select clear

> show #!13 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!13 models

> show #!6 models

> select #14/A:97

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.90725,0.31566,-0.27796,2.8054,0.29785,-0.01556,0.95449,-50.578,0.29696,-0.94875,-0.10814,46.454

> view matrix models
> #14,0.93295,0.28926,-0.21434,-0.73384,0.25781,-0.12123,0.95856,-50.42,0.25129,-0.94954,-0.18768,51.003

> view matrix models
> #14,0.95399,0.10503,0.28085,-26.454,-0.27841,-0.037495,0.95973,-44.999,0.11133,-0.99376,-0.0065275,43.104

> view matrix models
> #14,0.98633,-0.1547,0.056722,-15.368,-0.093531,-0.24224,0.9657,-47.262,-0.13566,-0.9578,-0.2534,58.309

> hide #!6 models

> show #4 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #4 models

> show #5 models

> hide #!6 models

> show #!6 models

> hide #5 models

> select #14/A:60

7 atoms, 6 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.98633,-0.1547,0.056722,5.0516,-0.093531,-0.24224,0.9657,-51.288,-0.13566,-0.9578,-0.2534,64.425

> view matrix models
> #14,0.98633,-0.1547,0.056722,10.913,-0.093531,-0.24224,0.9657,-51.526,-0.13566,-0.9578,-0.2534,63.602

> view matrix models
> #14,0.98633,-0.1547,0.056722,15.905,-0.093531,-0.24224,0.9657,-50.924,-0.13566,-0.9578,-0.2534,60.642

> ui mousemode right "rotate selected models"

> view matrix models
> #14,0.97926,-0.18136,0.090283,14.242,-0.086033,0.031182,0.9958,-52.444,-0.18342,-0.98292,0.014932,47.335

> select clear

> select #14/A:91

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view matrix models
> #14,0.90266,-0.17746,0.39205,-0.47885,-0.41831,-0.14782,0.8962,-44.018,-0.10109,-0.97296,-0.20766,57.936

> ui mousemode right "translate selected models"

> view matrix models
> #14,0.90266,-0.17746,0.39205,-2.5843,-0.41831,-0.14782,0.8962,-43.691,-0.10109,-0.97296,-0.20766,52.913

> select clear

> hide #!6 models

> show #!6 models

> select clear

Drag select of 26 atoms, 132 residues, 25 bonds  
Drag select of 40 atoms, 192 residues, 36 bonds  

> hide sel cartoons

> view matrix models
> #14,0.90266,-0.17746,0.39205,-4.6463,-0.41831,-0.14782,0.8962,-41.429,-0.10109,-0.97296,-0.20766,56.964

> select clear

[Repeated 1 time(s)]

> show #!3 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!3 models

> show #!3 models

> select #14/A

3671 atoms, 3705 bonds, 506 residues, 1 model selected  

> show sel cartoons

> select clear

> hide #!3 models

> open 3w78 fromDatabase pdb format mmcif

Summary of feedback from opening 3w78 fetched from pdb  
---  
notes | Fetching compressed mmCIF 3w78 from http://files.rcsb.org/download/3w78.cif  
Fetching CCD CBD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/CBD/CBD.cif  
Fetching CCD FMN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/FMN/FMN.cif  
  
3w78 title:  
Crystal Structure of azoreductase AzrC in complex with NAD(P)-inhibitor
Cibacron Blue [more info...]  
  
Chain information for 3w78 #15  
---  
Chain | Description | UniProt  
A B C D | FMN-dependent NADH-azoreductase | C0STY1_9BACI 1-211  
  
Non-standard residues in 3w78 #15  
---  
CBD — cibacron blue  
FMN — flavin mononucleotide (riboflavin monophosphate)  
  
3w78 mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  

> matchmaker #15 to #6

Computing secondary structure  
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 fold_azor_monomer_fad_model_0.cif, chain A (#6) with 3w78, chain A
(#15), sequence alignment score = 709.3  
RMSD between 188 pruned atom pairs is 0.720 angstroms; (across all 207 pairs:
1.539)  
  

> hide #!6 models

> select #15/A

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> select #15/C

1697 atoms, 1735 bonds, 217 residues, 1 model selected  

> select #15/C

1697 atoms, 1735 bonds, 217 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> select #15/D

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> show #!3 models

> hide #!14 models

> hide #!3 models

> select #15/A

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> rainbow sel

> select clear

> select #15/B

1696 atoms, 1735 bonds, 216 residues, 1 model selected  

> rainbow sel

> select clear

> show #!3 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> select #3/B:169

11 atoms, 11 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> select clear

> show #15 models

> hide #15 models

> show #15 models

> select #3/B:58

7 atoms, 6 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 7 atom styles  

> show sel atoms

> hide sel atoms

> select clear

> select #3/A:184

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> show sel atoms

> hide #!3 models

> show #!3 models

> hide #15 models

> select clear

> show #15 models

> select #15/B:52

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #4 models

> hide #4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> select #15/A:186

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> show sel atoms

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #4 models

> show #!3 models

> hide #4 models

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select clear

> select #15/A

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> show #!3 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #!3 models

> select #15/A

1698 atoms, 1735 bonds, 218 residues, 1 model selected  

> select #15/B

1696 atoms, 1735 bonds, 216 residues, 1 model selected  

> color sel light gray

> color sel gray

> select clear

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #15/B:52

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> show sel atoms

> show #!3 models

> hide #!3 models

> show #!3 models

> select #3/A:147

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 12 atom styles  

> show sel atoms

> hide sel atoms

> select clear

> hide #!3 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> select #3/B:127

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> show sel atoms

> select clear

> select #3/B:124

12 atoms, 12 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 12 atom styles  

> show sel atoms

> hide #!3 models

> show #!3 models

> select #3/B:122

11 atoms, 11 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> select #3/B:126

5 atoms, 4 bonds, 1 residue, 1 model selected  

> open 4m0C fromDatabase pdb format mmcif

Summary of feedback from opening 4m0C fetched from pdb  
---  
note | Fetching compressed mmCIF 4m0c from http://files.rcsb.org/download/4m0c.cif  
  
4m0c title:  
The crystal structure of a FMN-dependent NADH-azoreductase from Bacillus
anthracis str. Ames Ancestor in complex with FMN. [more info...]  
  
Chain information for 4m0c #16  
---  
Chain | Description | UniProt  
A B | FMN-dependent NADH-azoreductase 1 | AZOR1_BACAN 1-220  
  
Non-standard residues in 4m0c #16  
---  
FMN — flavin mononucleotide (riboflavin monophosphate)  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
ZN — zinc ion  
  

> hide #15 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #!3 models

> hide #!16 models

> show #15 models

> hide #15 models

> matchmaker #!16 to #3

Computing secondary structure  
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
(#16), sequence alignment score = 530.5  
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)  
  

> show #!16 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #15 models

> hide #!16 models

> show #!16 models

> hide #!16 models

> select #3/A:24

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> show sel atoms

> select #3/A:28

9 atoms, 8 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 9 atom styles  

> show sel atoms

> show #!16 models

> select #3/A:24@NZ

1 atom, 1 residue, 1 model selected  

> color (#!3 & sel) blue

> select clear

> hide #!3 models

> show #!3 models

> select #3/B:60

14 atoms, 15 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 14 atom styles  

> show sel atoms

> hide #!3 models

> show #!3 models

> hide #!3 models

> color #!16 bypolymer

> color #!16 bychain

> undo

> show #!14 models

> hide #!14 models

> view matrix models
> #3,0.14541,-0.27369,0.95076,11.699,0.94367,-0.25032,-0.21638,-0.059448,0.29722,0.92867,0.22188,0.19931

> view matrix models
> #3,0.14541,-0.27369,0.95076,11.468,0.94367,-0.25032,-0.21638,0.097978,0.29722,0.92867,0.22188,1.1612

> show #!3 models

> hide #!3 models

> view matrix models
> #3,0.14541,-0.27369,0.95076,11.206,0.94367,-0.25032,-0.21638,1.5618,0.29722,0.92867,0.22188,1.9041

> show #!3 models

> hide #!3 models

> show #15 models

> hide #!16 models

> hide #15 models

> show #15 models

> show #!16 models

> hide #15 models

> show #15 models

> hide #15 models

> show #15 models

> hide #!16 models

> show #!3 models

> hide #15 models

> view matrix models
> #3,0.14541,-0.27369,0.95076,3.1194,0.94367,-0.25032,-0.21638,-4.132,0.29722,0.92867,0.22188,5.8471

> select #/B

Expected an objects specifier or a keyword  

> select #3/B

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> rainbow sel

> select #3/A:85

9 atoms, 8 bonds, 1 residue, 1 model selected  

> show #5 models

> hide #!3 models

> show #!3 models

> show #!6 models

> hide #5 models

> hide #!3 models

> hide #!6 models

> show #8 models

> rainbow #8

> show #9 models

> hide #9 models

> show #9 models

> hide #8 models

> show #10 models

> hide #9 models

> rainbow #10

> show #9 models

> show #11 models

> hide #11 models

> ui tool show Matchmaker

> matchmaker #8-10 to #7

Computing secondary structure  
[Repeated 3 time(s)]  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 fold_icd_model_0.cif, chain A (#7) with fold_mqo_model_0.cif, chain
A (#8), sequence alignment score = 56  
RMSD between 7 pruned atom pairs is 1.546 angstroms; (across all 312 pairs:
34.056)  
  
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhc_model_0.cif,
chain A (#9), sequence alignment score = 55.5  
RMSD between 6 pruned atom pairs is 1.303 angstroms; (across all 235 pairs:
26.259)  
  
Matchmaker fold_icd_model_0.cif, chain A (#7) with fold_ndhf_model_0.cif,
chain A (#10), sequence alignment score = 38.2  
RMSD between 5 pruned atom pairs is 0.853 angstroms; (across all 135 pairs:
19.431)  
  

> view matrix models
> #3,0.14541,-0.27369,0.95076,8.5292,0.94367,-0.25032,-0.21638,-19.372,0.29722,0.92867,0.22188,0.15815

> hide #9 models

> show #11 models

> hide #10 models

> show #12 models

> hide #11 models

> hide #12 models

> show #7 models

> rainbow #7

> show #8 models

> hide #7 models

> show #7 models

> hide #8 models

> show #5 models

> hide #5 models

> show #!6 models

> hide #7 models

> show #7 models

> hide #!6 models

> show #!6 models

> hide #7 models

> show #7 models

> select #7/A:182

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #7,0.056929,0.94842,-0.31187,29.698,-0.99216,0.018927,-0.12355,27.519,-0.11127,0.31646,0.94206,-48.931

> ui mousemode right "rotate selected models"

> select #7/A:168

11 atoms, 11 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.6578,0.45453,-0.60058,25.727,0.50261,-0.85878,-0.099448,19.133,-0.56096,-0.23644,-0.79336,-49.882

> view matrix models
> #7,0.60118,0.48068,-0.63838,25.96,0.54786,-0.82948,-0.10864,18.796,-0.58175,-0.28444,-0.76201,-49.624

> view matrix models
> #7,0.49131,0.84301,-0.21895,27.321,0.79014,-0.53716,-0.29517,16.511,-0.36645,-0.027978,-0.93002,-51.657

> view matrix models
> #7,0.29276,0.89319,-0.34133,28.206,0.88387,-0.38897,-0.25975,15.859,-0.36478,-0.22565,-0.90334,-51.396

> view matrix models
> #7,0.39394,0.66509,-0.6344,27.076,0.74669,-0.63405,-0.20106,17.118,-0.53597,-0.3945,-0.7464,-49.757

> view matrix models
> #7,0.3975,0.64273,-0.6549,27.026,0.73208,-0.65243,-0.19596,17.242,-0.55323,-0.40155,-0.72986,-49.601

> view matrix models
> #7,0.31312,0.65044,-0.69202,27.453,0.7722,-0.59855,-0.21318,16.892,-0.55286,-0.46763,-0.68969,-49.434

> view matrix models
> #7,0.41324,0.50876,-0.75524,26.815,0.7267,-0.68404,-0.06317,17.64,-0.54875,-0.52273,-0.6524,-49.31

> select clear

> hide #7 models

> show #8 models

> select #8/A:495

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #8,-0.29707,0.95019,0.094245,27.561,-0.9516,-0.28647,-0.11132,28.24,-0.078773,-0.12275,0.98931,-51.568

> ui mousemode right "rotate selected models"

> select #8/A:464

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view matrix models
> #8,-0.83282,-0.06747,-0.54942,33.938,0.53295,-0.36591,-0.76293,29.175,-0.14956,-0.9282,0.3407,-46.42

> view matrix models
> #8,-0.79413,0.58208,0.17476,27.984,0.60087,0.79512,0.08207,22.702,-0.09118,0.17018,-0.98119,-32.86

> view matrix models
> #8,-0.74237,-0.25474,0.61968,22.54,0.1102,0.86588,0.48796,20.688,-0.66087,0.43053,-0.61473,-33.983

> view matrix models
> #8,-0.85203,0.52313,0.019577,29.536,0.49615,0.81887,-0.28859,26.523,-0.167,-0.23617,-0.95725,-33.383

> view matrix models
> #8,-0.82201,-0.085732,0.56298,23.565,0.39872,0.61921,0.67646,17.631,-0.4066,0.78053,-0.47481,-35.657

> view matrix models
> #8,-0.96452,-0.0076278,0.26388,26.924,0.094374,0.92356,0.37165,21.898,-0.24655,0.38337,-0.89008,-32.89

> view matrix models
> #8,-0.97869,-0.027577,0.20348,27.504,0.057976,0.91351,0.40267,21.719,-0.19698,0.40588,-0.89245,-33.004

> view matrix models
> #8,-0.96042,0.18076,0.21192,27.65,0.26575,0.82255,0.50278,19.967,-0.083434,0.5392,-0.83803,-33.708

> view matrix models
> #8,-0.94381,0.13924,0.29972,26.723,0.29173,0.77716,0.5576,19.31,-0.15529,0.61371,-0.77411,-33.957

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs

> hide #8 models

> show #!13 models

> hide #!13 models

> show #!14 models

> hide #!14 models

> show #!16 models

> open 1v4B fromDatabase pdb format mmcif

Summary of feedback from opening 1v4B fetched from pdb  
---  
notes | Fetching compressed mmCIF 1v4b from http://files.rcsb.org/download/1v4b.cif  
Fetching CCD IPA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/IPA/IPA.cif  
  
1v4b title:  
The crystal structure of AzoR (Azo Reductase) from Escherichia coli: Oxidized
form [more info...]  
  
Chain information for 1v4b #17  
---  
Chain | Description | UniProt  
A | NADH-azoreductase, FMN-dependent | ACPD_ECOLI 1-200  
  
Non-standard residues in 1v4b #17  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
FMN — flavin mononucleotide (riboflavin monophosphate)  
IPA — isopropyl alcohol (2-propanol)  
  
1v4b mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> open 2B3D fromDatabase pdb format mmcif

Summary of feedback from opening 2B3D fetched from pdb  
---  
note | Fetching compressed mmCIF 2b3d from http://files.rcsb.org/download/2b3d.cif  
  
2b3d title:  
Crystal structure of Modulator of Drug activity B in complex with flavin
adenine dinucleotide [more info...]  
  
Chain information for 2b3d #18  
---  
Chain | Description | UniProt  
A B | Modulator of drug activity B | MDAB_ECOLI 13-204  
  
Non-standard residues in 2b3d #18  
---  
FAD — flavin-adenine dinucleotide  
  

> hide #!16 models

> hide #!17 models

> matchmaker #!18 to #3

Computing secondary structure  
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain B
(#18), sequence alignment score = 156.9  
RMSD between 82 pruned atom pairs is 1.158 angstroms; (across all 168 pairs:
6.190)  
  

> show #!3 models

> hide #!6 models

> hide #!3 models

> show #!3 models

> hide #!18 models

> show #!6 models

> select /A

43169 atoms, 43600 bonds, 3 pseudobonds, 5896 residues, 20 models selected  

> hide #!3 models

> show #!3 models

> show #7 models

> hide #7 models

> hide #!6 models

> matchmaker #1,4-5,7-12,15#!2,6,13-14,16-18 & sel to #3 & sel

Computing secondary structure  
[Repeated 12 time(s)]  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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#6), sequence alignment score =
1081.4  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_nad_model_0.cif, chain A (#11), sequence alignment score =
1081.4  
RMSD between 208 pruned atom pairs is 0.436 angstroms; (across all 208 pairs:
0.436)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_model_0.cif, chain A (#2), sequence alignment score = 1085  
RMSD between 208 pruned atom pairs is 0.263 angstroms; (across all 208 pairs:
0.263)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_fad_model_0.cif, chain A (#4), sequence alignment score =
1081.4  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_dimer_nad_model_0.cif, chain A (#5), sequence alignment score =
1074.2  
RMSD between 208 pruned atom pairs is 0.269 angstroms; (across all 208 pairs:
0.269)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_icd_model_0.cif, chain A (#7), sequence alignment score = 83.4  
RMSD between 10 pruned atom pairs is 1.453 angstroms; (across all 169 pairs:
23.782)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_mqo_model_0.cif, chain A (#8), sequence alignment score = 59.8  
RMSD between 7 pruned atom pairs is 1.684 angstroms; (across all 65 pairs:
22.736)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhc_model_0.cif, chain A (#9), sequence alignment score = 65.4  
RMSD between 24 pruned atom pairs is 1.163 angstroms; (across all 154 pairs:
32.226)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_ndhf_model_0.cif, chain A (#10), sequence alignment score = 59.3  
RMSD between 31 pruned atom pairs is 1.111 angstroms; (across all 142 pairs:
21.293)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_suca_model_0.cif, chain A (#12), sequence alignment score = 85.2  
RMSD between 6 pruned atom pairs is 1.325 angstroms; (across all 101 pairs:
17.171)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 9h2i, chain A
(#13), sequence alignment score = 24  
RMSD between 11 pruned atom pairs is 0.322 angstroms; (across all 26 pairs:
11.957)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 8rx4, chain A
(#14), sequence alignment score = 51.5  
RMSD between 10 pruned atom pairs is 1.029 angstroms; (across all 173 pairs:
29.959)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 3w78, chain A
(#15), sequence alignment score = 716.5  
RMSD between 189 pruned atom pairs is 0.774 angstroms; (across all 207 pairs:
1.461)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 4m0c, chain A
(#16), sequence alignment score = 530.5  
RMSD between 170 pruned atom pairs is 0.951 angstroms; (across all 207 pairs:
2.146)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 1v4b, chain A
(#17), sequence alignment score = 427.4  
RMSD between 135 pruned atom pairs is 1.176 angstroms; (across all 194 pairs:
2.701)  
  
Matchmaker fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2b3d, chain A
(#18), sequence alignment score = 150.4  
RMSD between 82 pruned atom pairs is 1.208 angstroms; (across all 167 pairs:
6.224)  
  

> show #!6 models

> hide #!6 models

> show #!18 models

> hide #!3 models

> show #!3 models

> hide #!18 models

> show #!6 models

> show #!2 models

> hide #!6 models

> show #!6 models

> hide #!2 models

> hide #!3 models

> show #!18 models

> hide #!18 models

> show #!17 models

> show #!16 models

> hide #!16 models

> show #!18 models

> hide #!17 models

> view matrix models
> #1,0.84943,0.0048481,-0.52768,0.65374,-0.36539,0.72688,-0.5815,-14.996,0.38074,0.68675,0.6192,0.19483,#6,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#11,0.3554,0.83707,0.41595,-1.2763,0.68382,0.070534,-0.72623,-14.22,-0.63724,0.54254,-0.54734,0.48453,#2,-0.46068,-0.87689,-0.13724,12.214,-0.014771,-0.14703,0.98902,-16.145,-0.88745,0.45765,0.054778,1.5059,#3,-0.028746,-0.72374,0.68947,11.158,0.45997,-0.62197,-0.6337,-18.381,0.88747,0.29892,0.35078,3.9374,#4,-0.099903,-0.34408,-0.93361,-1.012,-0.5832,0.78048,-0.22524,-14.805,0.80616,0.52198,-0.27864,-1.5521,#5,0.22887,-0.90083,-0.36896,11.233,0.86356,0.36282,-0.35017,-15.736,0.44931,-0.23848,0.86096,4.0367,#7,0.46353,0.81912,0.33791,5.0029,-0.6474,0.57345,-0.50202,-21.729,-0.60499,0.013936,0.79611,6.3283,#8,-0.26206,-0.91936,-0.29342,-0.19912,0.46009,0.14825,-0.87541,-25.028,0.84832,-0.36441,0.38414,-10.304,#9,-0.36876,-0.75997,0.53522,0.42258,-0.57013,0.63969,0.5155,-25.953,-0.73415,-0.11505,-0.66917,-11.957,#10,-0.76439,0.47517,0.4358,-2.938,-0.63904,-0.46854,-0.60999,-30.867,-0.085662,-0.74477,0.6618,-2.3478,#12,0.5306,0.7007,0.47695,28.271,0.79647,-0.60467,0.0022843,-13.278,0.29,0.37867,-0.87893,-22.901,#13,-0.87207,0.20936,-0.44234,-12.953,-0.35472,-0.89312,0.27661,-70.145,-0.33715,0.39813,0.85313,-58.476,#14,0.06735,0.64492,0.76128,-46.484,-0.9052,0.36039,-0.22523,-11.844,-0.41961,-0.67394,0.60805,-31.123,#15,-0.96531,0.14882,-0.21456,-77.459,0.24373,0.21868,-0.94487,-1.6269,-0.093694,-0.96438,-0.24737,25.022,#16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786,#17,0.86185,-0.43699,0.25741,-7.1671,0.16099,0.71702,0.67821,-60.106,-0.48094,-0.54307,0.68831,13.982,#18,-0.37684,0.76002,-0.52949,10.529,0.34458,-0.41558,-0.84176,-4.7032,-0.8598,-0.49966,-0.10528,11.963

> show #1 models

> hide #!6 models

> hide #!18 models

> show #!6 models

> hide #1 models

> show #!3 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> select clear

> show #1 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #4 models

> hide #1 models

> show #!3 models

> hide #4 models

> show #1 models

> hide #!3 models

> show #!17 models

> hide #!17 models

> show #!18 models

> hide #1 models

> show #1 models

> show #!3 models

> hide #1 models

> hide #!3 models

> show #1 models

> hide #1 models

> select ::name="FAD"

477 atoms, 522 bonds, 9 residues, 6 models selected  

> show #!6 models

> hide #!6 models

> color sel & #!18 bychain

> undo

> select clear

> color #!18 bychain

> undo

> show #!3 models

> hide #!18 models

> show #!17 models

> hide #!17 models

> show #!17 models

> hide #!17 models

> show #!18 models

> hide #!3 models

> show #!3 models

> hide #!18 models

> show #!18 models

> hide #!3 models

> show #!6 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!3 models

> hide #!3 models

> show #!18 models

> show #1 models

> hide #!6 models

> hide #!18 models

> show #!18 models

> hide #!18 models

> show #!3 models

> hide #1 models

> select #3/A

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> select ::name="FAD"

477 atoms, 522 bonds, 9 residues, 6 models selected  

> select ~sel & ##selected

25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected  

> ui tool show "Color Actions"

> color sel tan

> color sel goldenrod

> select #3/B

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> rainbow sel

> select clear

> select ::name="FAD"

477 atoms, 522 bonds, 9 residues, 6 models selected  

> select ~sel & ##selected

25317 atoms, 24782 bonds, 1 pseudobond, 4185 residues, 7 models selected  

> color sel dark goldenrod

> color sel salmon

> color sel dark goldenrod

> color sel peru

> color sel dark orange

> color sel saddle brown

> color sel dark goldenrod

> color sel slate gray

> color sel steel blue

> color sel cadet blue

> color sel dark olive green

> select #3/B

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> rainbow sel

> select clear

> show #1 models

> hide #!3 models

> show #!13 models

> hide #!13 models

> show #!6 models

> hide #1 models

> show #1 models

> hide #!6 models

> show #4 models

> hide #1 models

> show #1 models

> hide #4 models

> show #4 models

> hide #1 models

> show #!3 models

> hide #!3 models

> show #1 models

> hide #4 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.png width
> 600 height 489 supersample 4 transparentBackground true

> show #4 models

> hide #1 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR-FAD.png
> width 600 height 489 supersample 4 transparentBackground true

> show #!3 models

> hide #4 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.png
> width 600 height 489 supersample 4 transparentBackground true

> select #3/A

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> show sel surfaces

> select clear

> select #3/B

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> hide #!3 models

> show #1 models

> show #!6 models

> hide #1 models

> show #1 models

> show #!3 models

> hide #!6 models

> hide #1 models

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.s.png
> width 600 height 489 supersample 4 transparentBackground true

> show #11 models

> hide #!3 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #12 models

> hide #12 models

> show #!6 models

> hide #11 models

> show #!2 models

> show #!3 models

> hide #!2 models

> hide #!6 models

> hide #!3 surfaces

> select add #3/B:123

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:122

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.png
> width 600 height 489 supersample 4 transparentBackground true

> select #3/B:123

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #3/B:122

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select add #3/B:124

23 atoms, 23 bonds, 2 residues, 2 models selected  

> select add #3/A:148

35 atoms, 35 bonds, 3 residues, 2 models selected  

> select add #3/A:184

43 atoms, 42 bonds, 4 residues, 3 models selected  

> select add #3/A:101@CA

44 atoms, 42 bonds, 5 residues, 3 models selected  

> select add #3/A:102@CB

45 atoms, 43 bonds, 6 residues, 3 models selected  

> select subtract #3/A:102

44 atoms, 43 bonds, 5 residues, 3 models selected  

> select add #3/A:102

52 atoms, 50 bonds, 6 residues, 3 models selected  

> select subtract #3/A:101

51 atoms, 49 bonds, 5 residues, 3 models selected  

> select add #3/A:101

59 atoms, 56 bonds, 6 residues, 3 models selected  

> select add #3/A:100

73 atoms, 71 bonds, 7 residues, 3 models selected  

> select add #3/A:99

81 atoms, 78 bonds, 8 residues, 3 models selected  

> select add #3/A:183

91 atoms, 88 bonds, 9 residues, 3 models selected  

> select add #3/A:143

97 atoms, 93 bonds, 10 residues, 3 models selected  

> select add #3/A:98

104 atoms, 100 bonds, 11 residues, 3 models selected  

> select add #3/A:19

110 atoms, 105 bonds, 12 residues, 3 models selected  

> select add #3/A:18

118 atoms, 112 bonds, 13 residues, 3 models selected  

> select add #3/A:17

124 atoms, 117 bonds, 14 residues, 3 models selected  

> select add #3/A:16

131 atoms, 123 bonds, 15 residues, 3 models selected  

> select add #3/A:9

136 atoms, 127 bonds, 16 residues, 3 models selected  

> select subtract #3/A:9

131 atoms, 123 bonds, 15 residues, 3 models selected  

> select add #3/A:8

138 atoms, 129 bonds, 16 residues, 3 models selected  

> select subtract #3/A:8

131 atoms, 123 bonds, 15 residues, 3 models selected  

> select add #3/A:10@CB

132 atoms, 123 bonds, 16 residues, 3 models selected  

> select subtract #3/A:10@CB

131 atoms, 123 bonds, 15 residues, 3 models selected  

> select add #3/A:10

141 atoms, 133 bonds, 16 residues, 3 models selected  

> select add #3/B:57

149 atoms, 140 bonds, 17 residues, 3 models selected  

> select add #3/B:52

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CG

158 atoms, 147 bonds, 19 residues, 3 models selected  

> select subtract #3/B:60@CG

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CG

158 atoms, 147 bonds, 19 residues, 3 models selected  

> select subtract #3/B:60@CG

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CG

158 atoms, 148 bonds, 19 residues, 3 models selected  

> select subtract #3/B:60@CG

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select subtract #3/B:52

149 atoms, 140 bonds, 17 residues, 3 models selected  

> select add #3/B:52

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CG

158 atoms, 147 bonds, 19 residues, 3 models selected  

> select subtract #3/B:60@CG

157 atoms, 147 bonds, 18 residues, 3 models selected  

> select add #3/B:60@CB

158 atoms, 147 bonds, 19 residues, 3 models selected  

> label (#!3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select #3/B:197

6 atoms, 5 bonds, 1 residue, 1 model selected  

> label height 3

> label height 2

> label height 1

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_FAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true

> show #5 models

> hide #!3 models

> select #5/B:123

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select #5/B:122

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select add #5/B:124

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select add #5/A:100

37 atoms, 39 bonds, 3 residues, 1 model selected  

> select add #5/A:101

45 atoms, 45 bonds, 4 residues, 1 model selected  

> select add #5/A:16

52 atoms, 51 bonds, 5 residues, 1 model selected  

> select add #5/A:10

62 atoms, 61 bonds, 6 residues, 1 model selected  

> select add #5/A:11

69 atoms, 68 bonds, 7 residues, 1 model selected  

> select subtract #5/A:11

62 atoms, 61 bonds, 6 residues, 1 model selected  

> select add #5/A:12

73 atoms, 72 bonds, 7 residues, 1 model selected  

> select add #5/B:60

87 atoms, 87 bonds, 8 residues, 1 model selected  

> select add #5/B:57

95 atoms, 94 bonds, 9 residues, 1 model selected  

> select add #5/B:58

102 atoms, 100 bonds, 10 residues, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> label height 1

[Repeated 1 time(s)]

> select clear

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select #5/B:113

8 atoms, 7 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 8 atom styles  

> show sel atoms

> show #4 models

> hide #4 models

> show #!3 models

> hide #!5 models

> show #4 models

> hide #4 models

> show #!5 models

> hide #!3 models

> hide sel atoms

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true

> hide #!5 models

> show #7 models

> hide #7 models

> show #11 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> select add #11/A:101

8 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #11/A:143

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select add #11/A:19

20 atoms, 18 bonds, 3 residues, 1 model selected  

> select add #11/A:18

28 atoms, 25 bonds, 4 residues, 1 model selected  

> select add #11/A:17

34 atoms, 30 bonds, 5 residues, 1 model selected  

> select add #11/A:10

44 atoms, 40 bonds, 6 residues, 1 model selected  

> select add #11/A:100

58 atoms, 55 bonds, 7 residues, 1 model selected  

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> label height 1

> select clear

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR_NAD.png
> width 600 height 489 supersample 4 transparentBackground true

> show #!5 models

> hide #!11 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.zoomin.label.png
> width 600 height 489 supersample 4 transparentBackground true

> ~label #5 residues

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoRx2_NAD.png
> width 600 height 489 supersample 4 transparentBackground true

> show #15 models

> hide #5 models

> show #4 models

> hide #4 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> select ::name="CBD"

204 atoms, 224 bonds, 4 residues, 1 model selected  

> color sel pale turquoise

> select clear

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/3w78.AzrC.CBD.FMN.png
> width 600 height 489 supersample 4 transparentBackground true

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> show #!3 models

> hide #15 models

> select #3/B:126

5 atoms, 4 bonds, 1 residue, 1 model selected  

> show #15 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #!3 models

> hide #15 models

> show #15 models

> hide #!3 models

> select #15/B:60

14 atoms, 15 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 14 atom styles  

> show sel atoms

> select clear

> show #!16 models

> hide #!16 models

> show #!16 models

> hide #15 models

> undo

> hide #!16 models

> show #!16 models

> hide #15 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs

> show #!6 models

> hide #!16 models

> show #1 models

> hide #!6 models

> show #!16 models

> hide #1 models

> show #!6 models

> hide #!16 models

> show #!16 models

> hide #!6 models

> show #1 models

> hide #!16 models

> show #!16 models

> hide #1 models

> show #!3 models

> hide #!16 models

> show #!16 models

> hide #!3 models

> select #16/B:126

6 atoms, 5 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 6 atom styles  

> show sel atoms

> show #5 models

> hide #5 models

> show #!17 models

> hide #!16 models

> show #1 models

> show #!3 models

> hide #!3 models

> show #!6 models

> hide #1 models

> hide #!6 models

> show #!6 models

> show #!3 models

> hide #!6 models

> hide #!17 models

> show #15 models

> hide #!3 models

> show #!16 models

> hide #15 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!16 models

> show #!3 models

> show #1 models

> hide #1 models

> show #7 models

> hide #7 models

> hide #!6 models

> show #1 models

> hide #!3 models

> show #5 models

> hide #5 models

> show #!6 models

> hide #!6 models

> hide #1 models

> show #7 models

> show #1 models

> hide #7 models

> show #7 models

> hide #1 models

> show #8 models

> hide #8 models

> show #8 models

> hide #7 models

> view matrix models
> #16,0.91421,0.39627,-0.084805,-8.1297,0.23794,-0.69429,-0.67923,-29.269,-0.32804,0.60077,-0.72901,-0.2786

> hide #8 models

> show #12 models

> hide #12 models

> show #9 models

> show #10 models

> hide #9 models

> show #!3 models

> hide #10 models

> select #3/A:104

11 atoms, 11 bonds, 1 residue, 1 model selected  

> style sel stick

Changed 11 atom styles  

> show sel atoms

> show #1 models

> hide #!3 models

> show #!3 models

> hide #1 models

> show #1 models

> hide #!3 models

> show #!3 models

> hide #1 models

> view matrix models
> #3,0.23414,-0.80222,0.54921,11.186,0.21867,-0.50698,-0.83376,-19.133,0.94729,0.31531,0.056721,3.3647

> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159

> open 2Bzs fromDatabase pdb format mmcif

Summary of feedback from opening 2Bzs fetched from pdb  
---  
notes | Fetching compressed mmCIF 2bzs from http://files.rcsb.org/download/2bzs.cif  
Fetching CCD CB1 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/CB1/CB1.cif  
  
2bzs title:  
Binding of anti-cancer prodrug CB1954 to the activating enzyme NQO2 revealed
by the crystal structure of their complex. [more info...]  
  
Chain information for 2bzs #19  
---  
Chain | Description | UniProt  
A B | NRH DEHYDROGENASE [QUINONE] 2 | NQO2_HUMAN 1-230  
  
Non-standard residues in 2bzs #19  
---  
CB1 — 5-(aziridin-1-yl)-2,4-dinitrobenzamide (CB1954; Tretazicar)  
FAD — flavin-adenine dinucleotide  
ZN — zinc ion  
  

> hide #!3 models

> color #!19 bychain

> view matrix models
> #3,0.40912,-0.74644,0.52483,11.372,0.17236,-0.50159,-0.84776,-19.225,0.89605,0.4373,-0.076559,3.0159

> show #!3 models

> hide #!3 models

> select #3/A

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> matchmaker #!19 to #3 & sel

Computing secondary structure  
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2bzs, chain B
(#19), sequence alignment score = 223.4  
RMSD between 70 pruned atom pairs is 1.017 angstroms; (across all 198 pairs:
5.647)  
  

> show #!3 models

> select clear

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #1 models

> hide #!19 models

> select #3/A

1646 atoms, 1685 bonds, 208 residues, 1 model selected  

> matchmaker #1 to #3 & sel

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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with
fold_azor_monomer_model_0.cif, chain A (#1), sequence alignment score = 1077.8  
RMSD between 208 pruned atom pairs is 0.467 angstroms; (across all 208 pairs:
0.467)  
  

> show #!19 models

> hide #1 models

> show #1 models

> hide #!3 models

> hide #!19 models

> show #!19 models

> select #19/B

2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected  

> rainbow sel

> hide #1 models

> show #4 models

> hide #4 models

> show #1 models

> select #19/B

2028 atoms, 1951 bonds, 4 pseudobonds, 365 residues, 2 models selected  

> color sel bychain

> select clear

> hide #1 models

> show #!3 models

> hide #!3 models

> show #4 models

> show #!3 models

> hide #4 models

> hide #!19 models

> show #!19 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #1 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!19 models

> hide #!19 models

> show #!19 models

> select clear

> open 2VPw fromDatabase pdb format mmcif

Summary of feedback from opening 2VPw fetched from pdb  
---  
notes | Fetching compressed mmCIF 2vpw from http://files.rcsb.org/download/2vpw.cif  
Fetching CCD MGD from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MGD/MGD.cif  
Fetching CCD MO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/MO/MO.cif  
Fetching CCD MQ7 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/7/MQ7/MQ7.cif  
  
2vpw title:  
Polysulfide reductase with bound menaquinone [more info...]  
  
Chain information for 2vpw #20  
---  
Chain | Description | UniProt  
A E | THIOSULFATE REDUCTASE | Q72LA4_THET2 1-765  
B F | NRFC PROTEIN | Q72LA5_THET2 1-195  
C G | HYPOTHETICAL MEMBRANE SPANNING PROTEIN | Q72LA6_THET2 0-252 1-253  
  
Non-standard residues in 2vpw #20  
---  
MGD —
2-amino-5,6-dimercapto-7-methyl-3,7,8A,9-tetrahydro-8-oxa-1,3,9,10-tetraaza-
anthracen-4-one guanosine dinucleotide (molybdopterin guanosine dinucleotide)  
MO — molybdenum atom  
MQ7 — menaquinone-7  
SF4 — iron/sulfur cluster  
  

> hide #!19 models

> hide #1 models

> hide #!20 surfaces

[Repeated 1 time(s)]

> hide #!20 atoms

> show #!20 cartoons

> matchmaker #!20 to #3 & sel

No 'to' model specified  

> matchmaker #!20 to #3

Computing secondary structure  
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 fold_azor_dimer_fad_model_0.cif, chain A (#3) with 2vpw, chain E
(#20), sequence alignment score = 78  
RMSD between 8 pruned atom pairs is 1.398 angstroms; (across all 148 pairs:
20.313)  
  

> show #!3 models

> hide #!3 models

> select /A

51617 atoms, 51746 bonds, 16 pseudobonds, 7421 residues, 24 models selected  

> rainbow sel & #!20

> select ::name="MQ7"

30 atoms, 32 bonds, 2 residues, 1 model selected  

> show sel surfaces

> open 7NZ1 fromDatabase pdb format mmcif

Summary of feedback from opening 7NZ1 fetched from pdb  
---  
notes | Fetching compressed mmCIF 7nz1 from http://files.rcsb.org/download/7nz1.cif  
Fetching CCD CSX from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/CSX/CSX.cif  
  
7nz1 title:  
Respiratory complex I from Escherichia coli - focused refinement of
cytoplasmic arm [more info...]  
  
Chain information for 7nz1 #21  
---  
Chain | Description | UniProt  
B | NADH-quinone oxidoreductase subunit B |   
D | NADH-quinone oxidoreductase subunit C/D | NUOCD_ECOLI 1-596  
E | NADH-quinone oxidoreductase subunit E | NUOE_ECOLI 1-166  
F | NADH-quinone oxidoreductase subunit F | NUOF_ECOLI 1-445  
G | NADH-quinone oxidoreductase subunit G | NUOG_ECOLI 1-908  
I | NADH-quinone oxidoreductase subunit I | NUOI_ECOLI 1-180  
  
Non-standard residues in 7nz1 #21  
---  
CA — calcium ion  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
SF4 — iron/sulfur cluster  
  

> hide sel atoms

> show sel cartoons

> hide #!20 models

> show #!21 cartoons

> hide #!21 atoms

> view matrix models
> #20,-0.20963,0.97025,0.12114,-159.27,0.41872,0.20104,-0.88558,-19.075,-0.88359,-0.13493,-0.44841,140.58

> color #!21 bychain

> matchmaker #!21 to #1

Computing secondary structure  
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 fold_azor_monomer_model_0.cif, chain A (#1) with 7nz1, chain G
(#21), sequence alignment score = 86.3  
RMSD between 22 pruned atom pairs is 0.859 angstroms; (across all 180 pairs:
20.357)  
  

> show #1 models

> select #21/G

7630 atoms, 7235 bonds, 24 pseudobonds, 1469 residues, 2 models selected  

> rainbow sel

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #!21 models

> show #!21 models

> hide #1 models

> matchmaker #!21 to #8

Computing secondary structure  
[Repeated 1 time(s)]  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 fold_mqo_model_0.cif, chain A (#8) with 7nz1, chain G (#21),
sequence alignment score = 63.6  
RMSD between 5 pruned atom pairs is 1.257 angstroms; (across all 362 pairs:
31.062)  
  

> show #8 models

> hide #!21 models

> hide #8 models

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_ankkflltv/fold_tcr_ankkflltv_model_4.cif

Chain information for fold_tcr_ankkflltv_model_0.cif #22  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_tcr_ankkflltv_model_1.cif #23  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_tcr_ankkflltv_model_2.cif #24  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_tcr_ankkflltv_model_3.cif #25  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_tcr_ankkflltv_model_4.cif #26  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Computing secondary structure  
[Repeated 4 time(s)]

> ui tool show Matchmaker

> matchmaker #23-26 to #22

Computing secondary structure  
[Repeated 4 time(s)]  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 fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_1.cif, chain B (#23), sequence alignment score = 581  
RMSD between 111 pruned atom pairs is 0.184 angstroms; (across all 111 pairs:
0.184)  
  
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_2.cif, chain B (#24), sequence alignment score =
573.8  
RMSD between 111 pruned atom pairs is 0.232 angstroms; (across all 111 pairs:
0.232)  
  
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_3.cif, chain B (#25), sequence alignment score = 581  
RMSD between 111 pruned atom pairs is 0.364 angstroms; (across all 111 pairs:
0.364)  
  
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_ankkflltv_model_4.cif, chain B (#26), sequence alignment score =
573.8  
RMSD between 110 pruned atom pairs is 0.269 angstroms; (across all 111 pairs:
0.332)  
  

> view matrix models
> #21,0.56571,0.78878,0.24042,-111.9,-0.81332,0.5818,0.0049461,-39.828,-0.13598,-0.19834,0.97066,-77.181

Drag select of 9 atoms, 113 residues, 8 bonds  

> open /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_0.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_1.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_2.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_3.cif
> /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/ChristineA/TCR/AgPredict/fold_tcr_demefteae/fold_tcr_demefteae_model_4.cif

Chain information for fold_tcr_demefteae_model_0.cif #27  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_tcr_demefteae_model_1.cif #28  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_tcr_demefteae_model_2.cif #29  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_tcr_demefteae_model_3.cif #30  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Chain information for fold_tcr_demefteae_model_4.cif #31  
---  
Chain | Description  
A | .  
B | .  
C | .  
  
Computing secondary structure  
[Repeated 4 time(s)]

> matchmaker #27-31 to #22

Computing secondary structure  
[Repeated 5 time(s)]  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 fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_0.cif, chain B (#27), sequence alignment score = 581  
RMSD between 111 pruned atom pairs is 0.323 angstroms; (across all 111 pairs:
0.323)  
  
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_1.cif, chain B (#28), sequence alignment score =
570.2  
RMSD between 111 pruned atom pairs is 0.204 angstroms; (across all 111 pairs:
0.204)  
  
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_2.cif, chain B (#29), sequence alignment score =
573.8  
RMSD between 111 pruned atom pairs is 0.345 angstroms; (across all 111 pairs:
0.345)  
  
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_3.cif, chain B (#30), sequence alignment score = 581  
RMSD between 111 pruned atom pairs is 0.287 angstroms; (across all 111 pairs:
0.287)  
  
Matchmaker fold_tcr_ankkflltv_model_0.cif, chain B (#22) with
fold_tcr_demefteae_model_4.cif, chain B (#31), sequence alignment score =
573.8  
RMSD between 111 pruned atom pairs is 0.349 angstroms; (across all 111 pairs:
0.349)  
  

> select clear

> delete atoms #22-31

> delete bonds #22-31

> show #!13 models

> save /Users/taic/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/MacBookPro021/project/AnuK/AzoR/AzoR.cxs

——— End of log from Wed Mar 11 15:25:43 2026 ———

opened ChimeraX session  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Model Number: Z15H00105LL/A
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6.1 (24G90)
      Kernel Version: Darwin 24.6.0
      Time since boot: 216 days, 2 hours, 57 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        DELL U2718Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
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Query Language

query: TracLinks and the [[TicketQuery]] macro both use a mini “query language” for specifying query filters. Filters are separated by ampersands (&). Each filter consists of the ticket field name, an operator and one or more values. More than one value are separated by a pipe (|), meaning that the filter matches any of the values. To include a literal & or | in a value, escape the character with a backslash (\).

The available operators are:

= the field content exactly matches one of the values
~= the field content contains one or more of the values
^= the field content starts with one of the values
$= the field content ends with one of the values

All of these operators can also be negated:

!= the field content matches none of the values
!~= the field content does not contain any of the values
!^= the field content does not start with any of the values
!$= the field content does not end with any of the values

The date fields created and modified can be constrained by using the = operator and specifying a value containing two dates separated by two dots (..). Either end of the date range can be left empty, meaning that the corresponding end of the range is open. The date parser understands a few natural date specifications like "3 weeks ago", "last month" and "now", as well as Bugzilla-style date specifications like "1d", "2w", "3m" or "4y" for 1 day, 2 weeks, 3 months and 4 years, respectively. Spaces in date specifications can be omitted to avoid having to quote the query string.

created=2007-01-01..2008-01-01 query tickets created in 2007
created=lastmonth..thismonth query tickets created during the previous month
modified=1weekago.. query tickets that have been modified in the last week
modified=..30daysago query tickets that have been inactive for the last 30 days

See also: TracTickets, TracReports, TracGuide, TicketQuery

Last modified 9 years ago Last modified on Jan 4, 2017, 10:45:36 AM
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