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#19776 closed defect (fixed)

kvfinder fails with "boxAtoms" option

Reported by:	pmcarlton@…	Owned by:	Eric Pettersen
Priority:	normal	Milestone:
Component:	Surface/Binding Analysis	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description (last modified by Eric Pettersen)

The following bug report has been submitted:
Platform:        macOS-15.6-arm64-arm-64bit
ChimeraX Version: 1.12.dev202601270036 (2026-01-27 00:36:36 UTC)
Description
trying to run "Find Cavities" - log reported successful install of kvfinder but the command returns:

ModuleNotFoundError: No module named '_pyKVFinder'

File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/kvfinder/prep.py", line 90, in prep_input
from _pyKVFinder import _filter_pdb

See log for complete Python traceback.


It seems something does get installed in 'Application Support':
>> ls  $HOME/Library/Application\ Support/ChimeraX/1.12/lib/python/site-packages/pyKVFinder
__init__.py                        _pyKVFinder.cpython-311-darwin.so* data/                              main.py
__pycache__/                       argparser.py                       grid/                              utils.py



Log:
UCSF ChimeraX version: 1.12.dev202601270036 (2026-01-27)  
© 2016-2026 Regents of the University of California. All rights reserved.  

> open /Users/pcarlton/Desktop/3A-work.cxs format session

Log from Wed Jan 28 16:58:23 2026UCSF ChimeraX version: 1.12.dev202601052311
(2026-01-05)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/pcarlton/Desktop/k00session.cxs format session

Log from Mon Jan 12 07:35:42 2026UCSF ChimeraX version: 1.12.dev202601052311
(2026-01-05)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/pcarlton/Desktop/acc-20251026/k00session.cxs

Log from Fri Sep 26 16:09:00 2025UCSF ChimeraX version: 1.11.dev202506162128
(2025-06-16)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/pcarlton/Desktop/chimerax/wow3.cxs

Log from Sat Sep 6 22:32:53 2025UCSF ChimeraX version: 1.11.dev202506162128
(2025-06-16)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open /Users/pcarlton/Desktop/wow.cxs

Log from Fri Sep 5 17:09:26 2025UCSF ChimeraX version: 1.11.dev202506132009
(2025-06-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/pcarlton/Downloads/fold_dsb_1_chk_2/fold_dsb_1_chk_2_model_0.cif

Chain information for fold_dsb_1_chk_2_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> open /Users/pcarlton/Downloads/fold_dsb_1_chk_2/fold_dsb_1_chk_2_model_4.cif

Chain information for fold_dsb_1_chk_2_model_4.cif #2  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/pcarlton/Downloads/fold_dsb_1_chk_2/fold_dsb_1_chk_2_model_3.cif

Chain information for fold_dsb_1_chk_2_model_3.cif #3  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/pcarlton/Downloads/fold_dsb_1_chk_2/fold_dsb_1_chk_2_model_2.cif

Chain information for fold_dsb_1_chk_2_model_2.cif #4  
---  
Chain | Description  
A | .  
B | .  
  

> open /Users/pcarlton/Downloads/fold_dsb_1_chk_2/fold_dsb_1_chk_2_model_1.cif

Chain information for fold_dsb_1_chk_2_model_1.cif #5  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  
[Repeated 3 time(s)]

> mmaker #5,4,3,2/B to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain B (#1) with
fold_dsb_1_chk_2_model_1.cif, chain B (#5), sequence alignment score = 2388.7  
RMSD between 387 pruned atom pairs is 0.493 angstroms; (across all 476 pairs:
22.599)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain B (#1) with
fold_dsb_1_chk_2_model_2.cif, chain B (#4), sequence alignment score = 2399.5  
RMSD between 275 pruned atom pairs is 0.544 angstroms; (across all 476 pairs:
22.976)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain B (#1) with
fold_dsb_1_chk_2_model_3.cif, chain B (#3), sequence alignment score = 2393.5  
RMSD between 293 pruned atom pairs is 0.667 angstroms; (across all 476 pairs:
18.255)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain B (#1) with
fold_dsb_1_chk_2_model_4.cif, chain B (#2), sequence alignment score = 2387.5  
RMSD between 266 pruned atom pairs is 0.428 angstroms; (across all 476 pairs:
32.072)  
  

> mmaker #5,4,3,2/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain A (#1) with
fold_dsb_1_chk_2_model_1.cif, chain A (#5), sequence alignment score = 1874.1  
RMSD between 45 pruned atom pairs is 0.675 angstroms; (across all 385 pairs:
42.674)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain A (#1) with
fold_dsb_1_chk_2_model_2.cif, chain A (#4), sequence alignment score = 1863.6  
RMSD between 102 pruned atom pairs is 0.370 angstroms; (across all 385 pairs:
42.971)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain A (#1) with
fold_dsb_1_chk_2_model_3.cif, chain A (#3), sequence alignment score = 1893.6  
RMSD between 16 pruned atom pairs is 1.156 angstroms; (across all 385 pairs:
42.030)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain A (#1) with
fold_dsb_1_chk_2_model_4.cif, chain A (#2), sequence alignment score = 1854.6  
RMSD between 12 pruned atom pairs is 1.416 angstroms; (across all 385 pairs:
56.468)  
  

> mmaker #5,4,3,2/B to #1/B

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain B (#1) with
fold_dsb_1_chk_2_model_1.cif, chain B (#5), sequence alignment score = 2388.7  
RMSD between 387 pruned atom pairs is 0.493 angstroms; (across all 476 pairs:
22.599)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain B (#1) with
fold_dsb_1_chk_2_model_2.cif, chain B (#4), sequence alignment score = 2399.5  
RMSD between 275 pruned atom pairs is 0.544 angstroms; (across all 476 pairs:
22.976)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain B (#1) with
fold_dsb_1_chk_2_model_3.cif, chain B (#3), sequence alignment score = 2393.5  
RMSD between 293 pruned atom pairs is 0.667 angstroms; (across all 476 pairs:
18.255)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain B (#1) with
fold_dsb_1_chk_2_model_4.cif, chain B (#2), sequence alignment score = 2387.5  
RMSD between 266 pruned atom pairs is 0.428 angstroms; (across all 476 pairs:
32.072)  
  

> color bychain

> sequence align /B

Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: LBXTEHCHG0IHUB1K  
Webservices job finished: LBXTEHCHG0IHUB1K  

> sequence header rmsd show

Chains used in RMSD evaluation for alignment 1: fold_dsb_1_chk_2_model_0.cif
#1/B, fold_dsb_1_chk_2_model_4.cif #2/B, fold_dsb_1_chk_2_model_3.cif #3/B,
fold_dsb_1_chk_2_model_2.cif #4/B, fold_dsb_1_chk_2_model_1.cif #5/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  

> sequence header conservation hide

Hiding conservation header for alignment 1  

> sequence align /A

Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Webservices job id: FM4FCOR4ASUZ530R  
Webservices job finished: FM4FCOR4ASUZ530R  

> sequence header 2 rmsd show

Chains used in RMSD evaluation for alignment 2: fold_dsb_1_chk_2_model_0.cif
#1/A, fold_dsb_1_chk_2_model_4.cif #2/A, fold_dsb_1_chk_2_model_3.cif #3/A,
fold_dsb_1_chk_2_model_2.cif #4/A, fold_dsb_1_chk_2_model_1.cif #5/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  

> sequence header 2 conservation hide

Hiding conservation header for alignment 2  

> select #1/A:301

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

> select #1/A:301 #2/A:301 #3/A:301 #4/A:301 #5/A:301

35 atoms, 30 bonds, 5 residues, 5 models selected  
Clustal Omega Alignment [ID: 2] region chain A..chain A [301] RMSD: 1.635  
  

> select #1/A:369-370

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

> select #1/A:369-382 #2/A:369-382 #3/A:369-382 #4/A:369-382 #5/A:369-382

500 atoms, 505 bonds, 70 residues, 5 models selected  
Clustal Omega Alignment [ID: 2] region chain A..chain A [369-382] RMSD: 0.597  
  

> select #1/A:301

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

> select #1/A:301-302 #2/A:301-302 #3/A:301-302 #4/A:301-302 #5/A:301-302

80 atoms, 75 bonds, 10 residues, 5 models selected  
Clustal Omega Alignment [ID: 2] region chain A..chain A [301-302] RMSD: 3.351  
  

> show sel atoms

> color sel byhetero

> select add /A:301-302

80 atoms, 75 bonds, 10 residues, 5 models selected  

> select #1/A:369

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

> select #1/A:369-383 #2/A:369-383 #3/A:369-383 #4/A:369-383 #5/A:369-383

540 atoms, 545 bonds, 75 residues, 5 models selected  
Clustal Omega Alignment [ID: 2] region chain A..chain A [369-383] RMSD: 0.678  
  

> mmaker #5,4,3,2/A & sel to #1/A & 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_dsb_1_chk_2_model_0.cif, chain A (#1) with
fold_dsb_1_chk_2_model_4.cif, chain A (#2), sequence alignment score = 70.5  
RMSD between 15 pruned atom pairs is 0.575 angstroms; (across all 15 pairs:
0.575)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain A (#1) with
fold_dsb_1_chk_2_model_3.cif, chain A (#3), sequence alignment score = 70.5  
RMSD between 15 pruned atom pairs is 0.520 angstroms; (across all 15 pairs:
0.520)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain A (#1) with
fold_dsb_1_chk_2_model_2.cif, chain A (#4), sequence alignment score = 70.5  
RMSD between 15 pruned atom pairs is 0.242 angstroms; (across all 15 pairs:
0.242)  
  
Matchmaker fold_dsb_1_chk_2_model_0.cif, chain A (#1) with
fold_dsb_1_chk_2_model_1.cif, chain A (#5), sequence alignment score = 64.5  
RMSD between 15 pruned atom pairs is 0.401 angstroms; (across all 15 pairs:
0.401)  
  

> select #1/B:322-323

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #1/B:323-338 #2/B:323-338 #3/B:323-338 #4/B:323-338 #5/B:323-338

610 atoms, 610 bonds, 80 residues, 5 models selected  
Clustal Omega Alignment [ID: 1] region chain B..chain B [323-338] RMSD: 5.381  
  

> select #1/B:340

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

> select #1/B:340-455 #2/B:340-455 #3/B:340-455 #4/B:340-455 #5/B:340-455

4675 atoms, 4795 bonds, 580 residues, 5 models selected  
Clustal Omega Alignment [ID: 1] region chain B..chain B [340-455] RMSD: 0.908  
  

> close

> open
> /Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif

Summary of feedback from opening
/Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 53  
Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' on line 33678  
  
Chain information for
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> clashes

No clashes  

> hide atoms

> show ribbons

> select Mg

4 atoms, 1 bond, 4 residues, 1 model selected  

> show sel atoms

Computing secondary structure  

> color sel orange

> style sel sphere

Changed 4 atom styles  

> select clear

> select /K:21

32 atoms, 33 bonds, 1 residue, 1 model selected  

> select add /J:44

64 atoms, 67 bonds, 2 residues, 1 model selected  

> select add /L:20

96 atoms, 101 bonds, 3 residues, 1 model selected  

> select up

3825 atoms, 4122 bonds, 120 residues, 1 model selected  

> color sel dark gray

> set bgColor white

> select clear

> select /K:30

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

> select add /L:1

65 atoms, 68 bonds, 2 residues, 1 model selected  

> hide sel cartoons

> show sel atoms

> color sel byhetero

> style sel ball

Changed 65 atom styles  

> select up

1898 atoms, 2036 bonds, 60 residues, 1 model selected  

> select down

65 atoms, 68 bonds, 2 residues, 1 model selected  

> contacts sel intraMol false

63 contacts  

> contacts sel intraMol false select true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    63 contacts
       atom1           atom2       overlap  distance
    /L DT 1 P     /B ARG 115 NH2    0.284    3.227
    /K DA 30 N1   /J DT 31 O2       0.243    2.862
    /K DA 30 N7   /L DT 1 C6        0.204    3.121
    /K DA 30 N3   /A TYR 230 HD2    0.169    2.456
    /L DT 1 C2    /K DA 30 N6       0.155    3.170
    /L DT 1 OP3   /K DA 30 OP2      0.115    2.885
    /L DT 1 O4'   /K DA 30 C5       0.084    3.116
    /L DT 1 H3    /J DA 30 C2       0.084    2.616
    /K DA 30 N3   /A TYR 230 CD2    0.062    3.263
    /L DT 1 N1    /K DA 30 N6       -0.000    3.250
    /L DT 1 O4'   /K DA 30 N7       -0.010    3.135
    /L DT 1 O4'   /K DA 30 C8       -0.025    3.225
    /L DT 1 H3    /J DA 30 H2       -0.046    2.046
    /L DT 1 N1    /K DA 30 C6       -0.054    3.379
    /K DA 30 N6   /L DT 1 N3        -0.059    3.309
    /L DT 1 O4'   /K DA 30 C4       -0.059    3.259
    /K DA 30 C5   /L DT 1 C1'       -0.065    3.465
    /K DA 30 C2   /A TYR 230 H      -0.084    2.784
    /L DT 1 N3    /J DA 30 C2       -0.086    3.411
    /L DT 1 N3    /J DA 30 H2       -0.107    2.732
    /L DT 1 P     /B ARG 115 HH22   -0.110    2.981
    /L DT 1 OP1   /B ARG 115 NH2    -0.119    2.859
    /L DT 1 OP3   /B ARG 115 NH2    -0.120    2.860
    /K DA 30 C5'  /A HIS 259 CG     -0.131    3.531
    /K DA 30 O3'  /H MG 1 MG        -0.136    2.166
    /K DA 30 C5'  /A HIS 259 CB     -0.137    3.537
    /L DT 1 C6    /K DA 30 C5       -0.138    3.538
    /K DA 30 H5'  /A HIS 259 ND1    -0.140    2.780
    /L DT 1 C1'   /K DA 30 C6       -0.172    3.572
    /L DT 1 C6    /K DA 30 N6       -0.175    3.500
    /L DT 1 N1    /K DA 30 C5       -0.177    3.502
    /K DA 30 N7   /L DT 1 H6        -0.180    2.805
    /K DA 30 H5'  /A HIS 259 CG     -0.188    2.888
    /K DA 30 N9   /L DT 1 O4'       -0.202    3.327
    /L DT 1 C5'   /B ARG 115 NH2    -0.216    3.556
    /L DT 1 H5''  /B ARG 115 NH2    -0.229    2.869
    /K DA 30 OP2  /L DT 1 OP2       -0.247    3.247
    /K DA 30 C6   /L DT 1 C2        -0.255    3.655
    /K DA 30 C2   /A TYR 230 HD2    -0.260    2.960
    /K DA 30 H2   /A TYR 230 H      -0.267    2.267
    /K DA 30 H2'  /L DT 1 C4'       -0.275    2.975
    /K DA 30 OP2  /L DT 1 P         -0.275    3.646
    /K DA 30 N6   /L DT 1 C4        -0.276    3.601
    /K DA 30 C2   /J DT 32 O2       -0.296    3.476
    /K DA 30 C2   /A TYR 230 N      -0.303    3.628
    /L DT 1 H5'   /K DA 30 H3'      -0.309    2.309
    /L DT 1 OP1   /B ARG 115 HH22   -0.317    2.417
    /L DT 1 OP1   /B ARG 115 CZ     -0.319    3.519
    /K DA 30 C5'  /A HIS 259 ND1    -0.323    3.663
    /K DA 30 C4'  /A HIS 259 CB     -0.330    3.730
    /K DA 30 H4'  /A HIS 259 HB3    -0.331    2.331
    /L DT 1 C5    /K DA 30 H62      -0.331    3.031
    /K DA 30 C4'  /A HIS 259 HB3    -0.337    3.037
    /L DT 1 C4    /K DA 30 H62      -0.339    3.039
    /L DT 1 C6    /K DA 30 C6       -0.349    3.749
    /K DA 30 N6   /L DT 1 C5        -0.359    3.684
    /K DA 30 N3   /A GLY 229 CA     -0.361    3.686
    /K DA 30 P    /L DT 1 OP3       -0.365    3.736
    /K DA 30 H4'  /A HIS 259 CB     -0.365    3.065
    /L DT 1 C6    /K DA 30 H62      -0.366    3.066
    /K DA 30 N7   /L DT 1 N1        -0.368    3.618
    /K DA 30 C3'  /L DT 1 H5'       -0.384    3.084
    /K DA 30 N3   /A TYR 230 H      -0.396    2.621
    

  
63 contacts  

> select up

228 atoms, 235 bonds, 10 residues, 1 model selected  

> style sel ball

Changed 228 atom styles  

> lighting flat

> color sel byhetero

> show sel cartoons

> nucleotides sel ladder

> nucleotides sel slab

> style nucleic & sel stick

Changed 161 atom styles  

> hide sel cartoons

> select clear

> hide atoms

> show cartoons

> select clear

> show cartoons

> select /A,B:115,230,259

121 atoms, 119 bonds, 6 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 121 atom styles  

> select clear

[Repeated 1 time(s)]

> hide atoms

[Repeated 1 time(s)]

> show cartoons

> select clear

> select /A,B:115,230,259

121 atoms, 119 bonds, 6 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> style sel sphere

Changed 121 atom styles  

> contacts sel select true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    178 contacts
         atom1            atom2       overlap  distance
    /B ARG 115 NH2   /L DT 1 P         0.284    3.227
    /B ARG 115 CD    /L DT 2 OP2       0.260    2.940
    /B HIS 259 ND1   /B LYS 316 NZ     0.232    3.033
    /B HIS 259 CE1   /J DA 28 O5'      0.199    3.001
    /A TYR 230 HD2   /K DA 30 N3       0.169    2.456
    /A ARG 115 CZ    /A GLN 128 OE1    0.164    3.016
    /B HIS 259 NE2   /J DA 28 P        0.155    3.341
    /A HIS 259 ND1   /A LYS 316 NZ     0.137    3.128
    /B HIS 259 ND1   /B LYS 316 HZ1    0.127    2.513
    /B HIS 259 CE1   /B LYS 316 NZ     0.119    3.206
    /A ARG 115 CD    /J DA 30 OP2      0.111    3.089
    /A HIS 259 ND1   /A LYS 316 HZ1    0.102    2.538
    /A ARG 115 HH12  /J DT 31 C7       0.093    2.607
    /B TYR 230 CD2   /J DA 28 N3       0.091    3.234
    /B ARG 115 NE    /B TYR 119 CE2    0.084    3.241
    /B ARG 115 NE    /B TYR 119 HE2    0.077    2.548
    /A TYR 230 CD2   /K DA 30 N3       0.062    3.263
    /B ARG 115 NH1   /B GLN 128 CD     0.033    3.307
    /B HIS 259 O     /B ILE 263 CD1    0.029    3.151
    /A ARG 115 NH1   /J DT 31 C7       0.026    3.299
    /B TYR 230 CE2   /J DA 28 N3       0.020    3.305
    /A ARG 115 NE    /J DA 30 OP2      0.011    2.714
    /B TYR 230 HD2   /J DA 28 N3       0.008    2.617
    /B ARG 115 CD    /L DT 2 P         -0.010    3.581
    /B HIS 259 CE1   /B LYS 316 HZ3    -0.023    2.723
    /B ARG 115 HD3   /L DT 2 P         -0.045    2.916
    /A ARG 115 NH1   /A GLN 128 OE1    -0.064    2.769
    /B ARG 115 O     /B TYR 118 HB3    -0.076    2.556
    /B ARG 115 HD2   /L DT 2 OP2       -0.076    2.576
    /A TYR 230 H     /K DA 30 C2       -0.084    2.784
    /B ARG 115 HD3   /L DT 2 OP1       -0.085    2.585
    /B ARG 115 C     /B TYR 118 H      -0.086    2.786
    /A ARG 115 C     /A TYR 118 H      -0.086    2.786
    /A ARG 115 NH1   /J DA 30 C8       -0.089    3.414
    /A ARG 115 CD    /A TYR 119 HE2    -0.089    2.789
    /B ARG 115 NH1   /B GLN 128 HB2    -0.089    2.729
    /A ARG 115 HH12  /J DT 31 H71      -0.096    2.096
    /A HIS 259 O     /A ILE 263 CD1    -0.098    3.278
    /A ARG 115 O     /A TYR 118 HB3    -0.105    2.585
    /B ARG 115 NH2   /B TYR 119 OH     -0.105    2.845
    /B HIS 259 O     /B ILE 263 HD12   -0.105    2.585
    /A ARG 115 HG3   /A GLN 128 CD     -0.106    2.806
    /B HIS 259 CD2   /J DA 28 O5'      -0.107    3.307
    /B ARG 115 HH22  /L DT 1 P         -0.110    2.981
    /B HIS 259 CG    /B LYS 316 HZ1    -0.111    2.811
    /A ARG 115 CD    /J DA 30 P        -0.119    3.690
    /B ARG 115 NH2   /L DT 1 OP1       -0.119    2.859
    /A ARG 115 CZ    /J DA 30 OP2      -0.120    3.320
    /B ARG 115 NH2   /L DT 1 OP3       -0.120    2.860
    /A TYR 230 HD1   /A PRO 231 HD2    -0.122    2.122
    /B ARG 115 HD3   /L DT 2 OP2       -0.127    2.627
    /A TYR 230 OH    /A GLU 262 OE1    -0.128    2.708
    /B ARG 115 NH2   /B TYR 119 CZ     -0.128    3.468
    /A HIS 259 CG    /K DA 30 C5'      -0.131    3.531
    /A ARG 115 HG3   /A GLN 128 NE2    -0.132    2.757
    /B ARG 115 NH1   /B TYR 118 CD2    -0.135    3.475
    /A HIS 259 CB    /K DA 30 C5'      -0.137    3.537
    /A ARG 115 HB2   /J DT 31 OP2      -0.138    2.638
    /B HIS 259 NE2   /J DA 28 O5'      -0.138    2.863
    /B ARG 115 HE    /B TYR 119 HE2    -0.140    2.140
    /A HIS 259 ND1   /K DA 30 H5'      -0.140    2.780
    /B TYR 230 OH    /B GLU 262 OE1    -0.145    2.725
    /B TYR 230 HE2   /J DA 28 N3       -0.145    2.770
    /A ARG 115 HD3   /A TYR 119 HE2    -0.148    2.148
    /B HIS 259 O     /B ILE 263 CG1    -0.149    3.329
    /A HIS 259 HB2   /A ASP 257 OD2    -0.156    2.636
    /A ARG 115 CD    /A TYR 119 CE2    -0.158    3.558
    /B HIS 259 HE2   /J DA 28 P        -0.167    3.038
    /A ARG 115 HD3   /J DA 30 OP2      -0.170    2.670
    /A TYR 230 CB    /A PRO 231 HD2    -0.178    2.878
    /A ARG 115 HE    /A TYR 119 OH     -0.187    2.287
    /A HIS 259 CG    /K DA 30 H5'      -0.188    2.888
    /A ARG 115 NH1   /A GLN 128 CD     -0.189    3.514
    /B ARG 115 NH1   /B GLN 128 OE1    -0.190    2.910
    /A ARG 115 NH1   /J DA 30 H3'      -0.194    2.819
    /B HIS 259 CE1   /B LYS 316 HZ1    -0.197    2.897
    /B HIS 259 CE1   /J DA 28 P        -0.201    3.772
    /B ARG 115 HE    /B TYR 119 CE2    -0.201    2.901
    /A HIS 259 CE1   /A LYS 316 NZ     -0.207    3.532
    /A ARG 115 NH1   /J DT 31 H71      -0.208    2.833
    /B HIS 259 NE2   /J DA 28 OP1      -0.208    2.933
    /B ARG 115 NH1   /B GLN 128 CB     -0.212    3.552
    /B ARG 115 O     /B TYR 118 CB     -0.212    3.392
    /A ARG 115 HE    /A TYR 119 CZ     -0.214    2.914
    /B ARG 115 NH2   /L DT 1 C5'       -0.216    3.556
    /A TYR 230 HD1   /A PRO 231 CD     -0.221    2.921
    /A TYR 230 CD1   /A PRO 231 HD2    -0.225    2.925
    /A ARG 115 O     /A TYR 119 CD2    -0.225    3.405
    /B ARG 115 NH2   /L DT 1 H5''      -0.229    2.869
    /B TYR 230 HE2   /J DA 28 H1'      -0.229    2.229
    /B ARG 115 C     /B TYR 118 N      -0.237    3.562
    /B HIS 259 O     /B ILE 263 HG13   -0.239    2.719
    /A ARG 115 NE    /A TYR 119 CE2    -0.244    3.569
    /B HIS 259 ND1   /J DA 28 C4'      -0.248    3.588
    /A HIS 259 O     /A ILE 263 CG1    -0.248    3.428
    /A TYR 230 HB3   /A PRO 231 CD     -0.250    2.950
    /A ARG 115 O     /A TYR 118 CB     -0.256    3.436
    /B ARG 115 NH1   /B TYR 118 CE2    -0.256    3.596
    /B HIS 259 ND1   /B LYS 316 HZ3    -0.258    2.898
    /A ARG 115 HE    /A TYR 119 CE2    -0.259    2.959
    /A TYR 230 HD2   /K DA 30 C2       -0.260    2.960
    /B ARG 115 HB3   /A THR 205 CG2    -0.260    2.960
    /B HIS 259 CG    /B LYS 316 NZ     -0.261    3.586
    /A ARG 115 NE    /J DA 30 P        -0.261    3.757
    /A ARG 115 CG    /A GLN 128 NE2    -0.266    3.591
    /A ARG 115 O     /A TYR 118 H      -0.267    2.347
    /A TYR 230 H     /K DA 30 H2       -0.267    2.267
    /A ARG 115 HD2   /J DT 31 OP2      -0.270    2.770
    /A ARG 115 C     /A TYR 118 N      -0.281    3.606
    /B HIS 259 HE2   /J DA 28 OP1      -0.283    2.383
    /A HIS 259 O     /A ILE 263 HD12   -0.284    2.764
    /A HIS 259 ND1   /A LYS 316 HZ3    -0.284    2.924
    /B HIS 259 CE1   /J DA 28 O4'      -0.285    3.485
    /B ARG 115 O     /B TYR 118 N      -0.285    2.990
    /A HIS 259 O     /A ILE 263 HG13   -0.287    2.767
    /A ARG 115 HG2   /A TYR 119 CE2    -0.287    2.987
    /B TYR 230 CB    /L DT 4 H1'       -0.288    2.988
    /B ARG 115 CZ    /B TYR 119 CE2    -0.288    3.689
    /A ARG 115 HB3   /B THR 205 CG2    -0.289    2.989
    /A TYR 230 CD1   /A ILE 263 HG12   -0.291    2.991
    /A ARG 115 HH11  /J DA 30 H3'      -0.294    2.294
    /B ARG 115 C     /B LEU 117 H      -0.294    2.994
    /A ARG 115 HB3   /B THR 205 HG21   -0.295    2.295
    /A ARG 115 CB    /J DT 31 OP2      -0.297    3.497
    /A TYR 230 CD1   /A PRO 231 CD     -0.299    3.699
    /B ARG 115 CD    /L DT 2 OP1       -0.300    3.500
    /B ARG 115 HG2   /B TYR 119 CE2    -0.302    3.002
    /B TYR 230 CD2   /J DA 28 C2       -0.303    3.703
    /B ARG 115 CG    /B TYR 119 CE2    -0.303    3.703
    /A TYR 230 N     /K DA 30 C2       -0.303    3.628
    /B TYR 230 O     /B GLY 229 O      -0.307    3.267
    /A ARG 115 HH11  /J DT 31 OP2      -0.308    2.408
    /A TYR 230 CD1   /A ILE 263 CG1    -0.310    3.710
    /B ARG 115 HB3   /A THR 205 HG21   -0.312    2.312
    /A TYR 230 CE1   /A ILE 263 CG1    -0.312    3.712
    /A ARG 115 HD3   /J DA 30 P        -0.313    3.184
    /A ARG 115 CD    /J DA 30 O5'      -0.313    3.513
    /B ARG 115 O     /B TYR 118 H      -0.315    2.395
    /A ARG 115 CG    /A TYR 119 CE2    -0.316    3.716
    /B ARG 115 HH22  /L DT 1 OP1       -0.317    2.417
    /B ARG 115 CZ    /L DT 1 OP1       -0.319    3.519
    /A ARG 115 NH1   /A GLN 128 NE2    -0.322    3.572
    /A HIS 259 ND1   /K DA 30 C5'      -0.323    3.663
    /A ARG 115 O     /A TYR 118 N      -0.324    3.029
    /A ARG 115 C     /A LEU 117 H      -0.326    3.026
    /A ARG 115 HD3   /A TYR 119 CE2    -0.327    3.027
    /A HIS 259 CB    /K DA 30 C4'      -0.330    3.730
    /A HIS 259 HB3   /K DA 30 H4'      -0.331    2.331
    /A TYR 230 HB3   /A PRO 231 HD2    -0.333    2.333
    /A HIS 259 HB3   /K DA 30 C4'      -0.337    3.037
    /B HIS 259 HB2   /B ASP 257 OD2    -0.338    2.818
    /B ARG 115 O     /B TYR 119 H      -0.345    2.425
    /B TYR 230 HD2   /J DA 28 C2       -0.345    3.045
    /A ARG 115 HH12  /J DA 30 C8       -0.348    3.048
    /A HIS 259 CE1   /A LYS 316 HZ3    -0.348    3.048
    /B ARG 115 NH1   /B GLN 128 CG     -0.352    3.692
    /B ARG 115 HG2   /B TYR 119 CD2    -0.353    3.053
    /A ARG 115 NE    /A TYR 119 HE2    -0.354    2.979
    /B TYR 230 HA    /B PRO 231 HD3    -0.357    2.357
    /A HIS 259 CB    /A ASP 257 OD2    -0.358    3.538
    /B TYR 230 CE2   /J DA 28 H1'      -0.362    3.062
    /B ARG 115 O     /B TYR 118 CA     -0.363    3.543
    /A ARG 115 CG    /A GLN 128 CD     -0.365    3.765
    /A HIS 259 CB    /K DA 30 H4'      -0.365    3.065
    /B ARG 115 O     /B TYR 119 HD2    -0.370    2.850
    /B TYR 230 CB    /L DT 4 C1'       -0.376    3.776
    /A HIS 259 CE1   /K DA 29 H4'      -0.378    3.078
    /B ARG 115 CZ    /B TYR 119 OH     -0.380    3.580
    /A HIS 259 N     /A ASP 257 CG     -0.381    3.706
    /B HIS 259 CD2   /J DA 28 OP1      -0.383    3.583
    /A ARG 115 O     /A TYR 119 HD2    -0.385    2.865
    /A ARG 115 NH1   /J DA 30 C3'      -0.389    3.714
    /B ARG 115 O     /B TYR 119 CD2    -0.391    3.571
    /B ARG 115 NE    /L DT 2 P         -0.393    3.889
    /A ARG 115 NE    /A TYR 119 CZ     -0.394    3.719
    /B TYR 230 HD1   /B PRO 231 HD2    -0.395    2.395
    /A TYR 230 H     /K DA 30 N3       -0.396    2.621
    /A HIS 259 H     /A ASP 257 C      -0.396    3.096
    

  
178 contacts  

> color sel byhetero

> select up

733 atoms, 740 bonds, 35 residues, 1 model selected  

> color sel byhetero

> style sel ball

Changed 733 atom styles  

> nucleotides sel tube/slab shape muffler

> open
> /Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif

Summary of feedback from opening
/Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 53  
Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' on line 33680  
  
Chain information for
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> open
> /Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif

Summary of feedback from opening
/Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 53  
Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' on line 33675  
  
Chain information for
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> open
> /Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif

Summary of feedback from opening
/Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 53  
Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' on line 33674  
  
Chain information for
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> open
> /Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif

Summary of feedback from opening
/Users/pcarlton/dsb123split/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 53  
Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' on line 33680  
  
Chain information for
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide sel atoms

[Repeated 1 time(s)]

> select #3/C:138@H

1 atom, 1 residue, 1 model selected  

> select clear

> hide atoms

> show cartoons

Computing secondary structure  
[Repeated 3 time(s)]

> mmaker #5,4,3,2/A to #1/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif, chain A
(#1) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif, chain A
(#5), sequence alignment score = 2085.4  
RMSD between 329 pruned atom pairs is 0.414 angstroms; (across all 425 pairs:
23.380)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif, chain A
(#1) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif, chain A
(#4), sequence alignment score = 2019.4  
RMSD between 317 pruned atom pairs is 0.430 angstroms; (across all 425 pairs:
24.391)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif, chain A
(#1) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif, chain A
(#3), sequence alignment score = 2032.6  
RMSD between 336 pruned atom pairs is 0.348 angstroms; (across all 425 pairs:
34.779)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif, chain A
(#1) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif, chain A
(#2), sequence alignment score = 2059  
RMSD between 334 pruned atom pairs is 0.363 angstroms; (across all 425 pairs:
34.100)  
  

> mmaker #5,4,3,2/A,B to #1/A,B pairing bs

Specify a single 'to' chain only  

> mmaker #5,4,3,2/A,B to #1/A,B pairing ss

Different number of reference/match chains (2 ref, 8 match)  

> select clear

[Repeated 1 time(s)]

> color bychain

> sequence align /A /B

Alignment identifier is 1  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1  
Webservices job id: HYO909XY9PEP5EGN  
Webservices job finished: HYO909XY9PEP5EGN  

> sequence header conservation hide

Hiding conservation header for alignment 1  

> sequence header rmsd show

Chains used in RMSD evaluation for alignment 1:
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/B,
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/B,
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/B,
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/B,
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/B  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  

> select #1/A:369-370

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select #1/A-B:232-370 #2/A-B:232-370 #3/A-B:232-370 #4/A-B:232-370
> #5/A-B:232-370

23000 atoms, 23280 bonds, 26 pseudobonds, 1390 residues, 6 models selected  

> select #1/A-B:231-370 #2/A-B:231-370 #3/A-B:231-370 #4/A-B:231-370
> #5/A-B:231-370

23140 atoms, 23430 bonds, 26 pseudobonds, 1400 residues, 6 models selected  
Clustal Omega Alignment [ID: 1] region chain A..chain B [231-370] RMSD: 0.559  
  

> select #1/A:37

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

> select #1/A-B:37-161 #2/A-B:37-161 #3/A-B:37-161 #4/A-B:37-161 #5/A-B:37-161

20696 atoms, 20826 bonds, 58 pseudobonds, 1250 residues, 6 models selected  
Clustal Omega Alignment [ID: 1] region chain A..chain B [37-161] RMSD: 0.557  
  

> select /A,B:37-368

54486 atoms, 54996 bonds, 103 pseudobonds, 3320 residues, 6 models selected  

> sequence chain #1/A,B#2/A,B#3/A,B#4/A,B#5/A,B

Alignment identifier is 2  

> select up

60496 atoms, 61081 bonds, 103 pseudobonds, 3722 residues, 6 models selected  

> select down

54486 atoms, 54996 bonds, 103 pseudobonds, 3320 residues, 6 models selected  

> select clear

[Repeated 1 time(s)]

> sequence align /J

Must specify 2 or more protein sequences  

> sequence align /C

Alignment identifier is 2  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2  
Webservices job id: 3GJNJYHZ4M8OOQXK  
Webservices job finished: 3GJNJYHZ4M8OOQXK  

> sequence header 2 conservation hide

Hiding conservation header for alignment 2  

> sequence header 2 rmsd show

Chains used in RMSD evaluation for alignment 2:
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C,
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C,
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C,
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C,
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  

> select #1/C:121

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/C:121-132 #2/C:121-132 #3/C:121-132 #4/C:121-132 #5/C:121-132

1055 atoms, 1065 bonds, 60 residues, 5 models selected  
Clustal Omega Alignment [ID: 2] region chain C..chain C [121-132] RMSD: 0.808  
  

> color sel orange red

> select add #4/C:120

1069 atoms, 1078 bonds, 61 residues, 5 models selected  
Drag select of 6 residues  
Drag select of 7 residues  

> select up

1561 atoms, 1574 bonds, 95 residues, 5 models selected  

> select down

1083 atoms, 1078 bonds, 62 residues, 5 models selected  

> color sel orange red

> color sel cornflower blue

> select #1/C:120

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #1/C:120-134 #2/C:120-134 #3/C:120-134 #4/C:120-134 #5/C:120-134

1195 atoms, 1205 bonds, 75 residues, 5 models selected  
Clustal Omega Alignment [ID: 2] region chain C..chain C [120-134] RMSD: 1.293  
  

> color sel cornflower blue

> contacts sel intraMol false interModel false select true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    161 contacts
                                       atom1                                                                       atom2                                     overlap  distance
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C TYR 125 HE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A ALA 86 O      0.129    2.351
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TYR 125 HE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A ALA 86 O      0.114    2.366
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TYR 125 HE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A ALA 86 O      0.106    2.374
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TYR 125 CE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A ALA 86 O      0.101    3.079
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TYR 125 CE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A ALA 86 O      0.079    3.101
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C TYR 125 CE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A ALA 86 O      0.074    3.106
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TYR 125 CE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A ALA 86 O      0.055    3.125
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C ASN 120 C     fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A MET 62 CE     0.048    3.352
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TRP 124 CZ3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A LEU 92 CD2    0.047    3.353
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C ASN 120 O     fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A MET 62 CE     0.046    3.134
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TYR 125 HE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A ALA 86 O      0.046    2.434
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C THR 121 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A ASP 93 OD1    0.038    3.142
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TRP 124 HH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A THR 85 C      0.034    2.666
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C TRP 124 HH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A THR 85 C      0.030    2.670
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TRP 124 HH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A THR 85 C      0.027    2.673
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C ASN 120 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A MET 62 CE     0.011    3.389
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C THR 121 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A ASP 93 OD1    0.004    3.176
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TRP 124 CZ3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LEU 92 CD2    0.001    3.399
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C ASN 120 C     fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A MET 62 CE     -0.005    3.405
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TRP 124 CZ3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A LEU 92 CD2    -0.026    3.426
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C TRP 124 HH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A THR 85 O      -0.037    2.517
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TRP 124 CZ3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A LEU 92 CD2    -0.052    3.452
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C THR 121 CG2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A ASP 93 OD1    -0.070    3.250
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C THR 121 HG21  fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A ASP 93 OD1    -0.073    2.553
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C THR 121 HG21  fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A ASP 93 OD1    -0.085    2.565
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C THR 121 CG2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A ASP 93 OD1    -0.092    3.272
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TRP 124 HZ3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LEU 92 CD2    -0.092    2.792
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TRP 124 HH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A THR 85 C      -0.094    2.794
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TRP 124 CH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A THR 85 C      -0.098    3.498
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C THR 121 OG1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A ASP 93 OD1    -0.103    2.683
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TYR 125 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LYS 89 CD     -0.104    3.504
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C ASN 120 C     fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A MET 62 SD     -0.106    3.588
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TYR 125 HE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A ALA 86 O      -0.107    2.587
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TRP 124 HH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A THR 85 C      -0.117    2.817
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C VAL 128 CG2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A GLU 66 O      -0.118    3.298
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TYR 125 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A LYS 89 HD2    -0.124    2.824
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TYR 125 CD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LYS 89 CD     -0.128    3.528
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TYR 125 CD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LYS 89 HD2    -0.132    2.832
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C THR 121 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A ASP 93 OD1    -0.135    3.315
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C TRP 124 CH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A THR 85 C      -0.140    3.540
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TYR 125 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LYS 89 HD2    -0.142    2.842
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C ASN 120 HB3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A MET 62 CE     -0.147    2.847
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TRP 124 CH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A THR 85 C      -0.148    3.548
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C TRP 124 CH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A THR 85 O      -0.152    3.332
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TYR 125 CE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A ALA 86 O      -0.153    3.333
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C THR 121 CG2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A MET 62 SD     -0.161    3.643
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C ASN 120 HB3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A MET 62 SD     -0.169    2.951
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C TRP 124 CZ3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A LEU 92 CD2    -0.170    3.570
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C ASN 120 HD21  fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LYS 59 HE3    -0.171    2.171
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C TRP 124 CZ2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A LEU 69 HG     -0.177    2.877
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C ASN 120 O     fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A MET 62 CE     -0.178    3.358
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TRP 124 HH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A THR 85 O      -0.185    2.665
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C THR 121 OG1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A ASP 93 OD1    -0.188    2.768
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TRP 124 CH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A ALA 86 N      -0.191    3.516
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TRP 124 HH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A ALA 86 N      -0.195    2.820
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TYR 125 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A LYS 89 HD2    -0.196    2.896
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TRP 124 CZ2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A LEU 69 HG     -0.197    2.897
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C TYR 125 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A LYS 89 HD2    -0.197    2.897
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C THR 121 HG21  fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A ASP 93 OD1    -0.199    2.679
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TYR 125 CD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A ALA 86 O      -0.201    3.381
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TYR 125 CD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A LYS 89 HD2    -0.207    2.907
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TRP 124 CZ2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A LEU 69 HG     -0.212    2.912
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C THR 121 CG2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A ASP 93 OD1    -0.213    3.393
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C ASN 120 ND2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LYS 59 HE3    -0.220    2.845
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TRP 124 HZ3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A LEU 92 CD2    -0.220    2.920
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TYR 125 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A LYS 89 HD2    -0.224    2.924
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C ASP 122 OD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LYS 89 CE     -0.226    3.406
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TRP 124 HE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A GLU 66 O      -0.227    2.307
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TRP 124 HH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A THR 85 O      -0.227    2.707
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TYR 125 CD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A LYS 89 HD2    -0.228    2.928
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TYR 125 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A LYS 89 CD     -0.229    3.629
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C THR 121 HG22  fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A MET 62 SD     -0.229    3.011
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TRP 124 CZ2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A LEU 69 HG     -0.230    2.930
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C ASN 120 ND2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LYS 59 HG3    -0.240    2.865
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TRP 124 CH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A THR 85 C      -0.242    3.642
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C TYR 125 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A LYS 89 HD2    -0.244    2.944
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TYR 125 CD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A ALA 86 O      -0.245    3.425
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C VAL 128 CG2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A GLU 66 O      -0.250    3.430
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/C ASP 122 OD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #1/A LYS 89 HZ1    -0.259    2.339
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/C TRP 124 CH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif #2/A THR 85 C      -0.261    3.661
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/C ASN 120 O     fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif #4/A MET 62 SD     -0.263    3.525
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TYR 125 CD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A ALA 86 O      -0.265    3.445
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C TRP 124 HE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A GLU 66 O      -0.267    2.347
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/C TRP 124 CD1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif #5/A MET 62 HA     -0.270    2.970
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/C ASN 120 C     fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif #3/A MET 62 HE1    -0.272    2.972
[deleted to fit within ticket limits]


> select up

1359 atoms, 1368 bonds, 81 residues, 9 models selected  

> select up

61582 atoms, 62167 bonds, 3825 residues, 9 models selected  

> select clear

> select #8

33549 atoms, 34136 bonds, 16 pseudobonds, 1984 residues, 2 models selected  

> show ribbons

> show sel ribbons

> select clear

> undo

[Repeated 1 time(s)]

> select clear

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

Drag select of 201 residues  

> select up

5003 atoms, 5015 bonds, 308 residues, 18 models selected  

> select up

53648 atoms, 54296 bonds, 3465 residues, 18 models selected  

> select up

301964 atoms, 307254 bonds, 17856 residues, 18 models selected  

> select clear

> select #1-11/dsb1A #1-11/dsb1B

59610 atoms, 60330 bonds, 3850 residues, 10 models selected  

> changechains sel dsb1X

Chain IDs of 3850 residues changed  

> select clear

> color #!1-5,7,9-11 bychain

> select clear

Drag select of 131 residues  

> select up

3040 atoms, 3041 bonds, 192 residues, 4 models selected  

> select up

17630 atoms, 17806 bonds, 1120 residues, 4 models selected  

> select #1-11/dsb2

44074 atoms, 44514 bonds, 2800 residues, 10 models selected  

> select #1-11/dsb2:1-100

16245 atoms, 16395 bonds, 1000 residues, 10 models selected  

> show sel & #!1-5,7,9-11 cartoons

> select clear

> select #1-11/dsb2:1-100

16245 atoms, 16395 bonds, 1000 residues, 10 models selected  

> show sel ribbons

> select clear

[Repeated 1 time(s)]

> color #!1-5,7,9-11 bychain

> select /dsb1X

59610 atoms, 60330 bonds, 3850 residues, 10 models selected  

> color (#!1-5,7,9-11 & sel) red

> select clear

Drag select of 158 residues  

> select up

8689 atoms, 8784 bonds, 523 residues, 9 models selected  

> select up

61582 atoms, 62167 bonds, 3825 residues, 9 models selected  

> info chains sel

chain id #1/spo11B2 chain_id spo11B2  
chain id #2/spo11B2 chain_id spo11B2  
chain id #3/spo11B2 chain_id spo11B2  
chain id #4/spo11B2 chain_id spo11B2  
chain id #5/spo11B2 chain_id spo11B2  
chain id #7/spo11B2 chain_id spo11B2  
chain id #9/spo11B2 chain_id spo11B2  
chain id #10/spo11B2 chain_id spo11B2  
chain id #11/spo11B2 chain_id spo11B2  

> changechains sel spo11B

Chain IDs of 3825 residues changed  

> select /spo11X

61575 atoms, 62160 bonds, 46 pseudobonds, 3825 residues, 10 models selected  

> select /spo11A

Nothing selected  
Drag select of 157 residues  

> select up

7696 atoms, 7791 bonds, 472 residues, 9 models selected  

> select up

61582 atoms, 62167 bonds, 3825 residues, 9 models selected  

> info chains sel

chain id #1/spo11B chain_id spo11B  
chain id #2/spo11B chain_id spo11B  
chain id #3/spo11B chain_id spo11B  
chain id #4/spo11B chain_id spo11B  
chain id #5/spo11B chain_id spo11B  
chain id #7/spo11B chain_id spo11B  
chain id #9/spo11B chain_id spo11B  
chain id #10/spo11B chain_id spo11B  
chain id #11/spo11B chain_id spo11B  

> select #3/spo11B:88

24 atoms, 23 bonds, 1 residue, 1 model selected  
Drag select of 44 residues  

> select up

4507 atoms, 4522 bonds, 265 residues, 9 models selected  

> select up

61582 atoms, 62167 bonds, 3825 residues, 9 models selected  

> changechains sel spo11aa

Chain IDs of 3825 residues changed  
Drag select of 19 residues  

> select up

3606 atoms, 3649 bonds, 245 residues, 9 models selected  

> select up

61575 atoms, 62160 bonds, 3825 residues, 9 models selected  

> changechains sel spo11bb

Chain IDs of 3825 residues changed  

> select /spo11aa

61582 atoms, 62167 bonds, 53 pseudobonds, 3825 residues, 10 models selected  

> mmaker #1,2,3,4,5,7,8,9,10/spo11aa to #11/spo11aa

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_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_4.um.cif, chain
spo11aa (#11) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif,
chain spo11aa (#1), sequence alignment score = 2051.2  
RMSD between 331 pruned atom pairs is 0.449 angstroms; (across all 425 pairs:
35.661)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_4.um.cif, chain
spo11aa (#11) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_1.um.cif,
chain spo11aa (#2), sequence alignment score = 2051.8  
RMSD between 333 pruned atom pairs is 0.408 angstroms; (across all 425 pairs:
20.832)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_4.um.cif, chain
spo11aa (#11) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_2.um.cif,
chain spo11aa (#3), sequence alignment score = 2058.4  
RMSD between 332 pruned atom pairs is 0.523 angstroms; (across all 425 pairs:
22.312)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_4.um.cif, chain
spo11aa (#11) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_3.um.cif,
chain spo11aa (#4), sequence alignment score = 2018.8  
RMSD between 330 pruned atom pairs is 0.572 angstroms; (across all 425 pairs:
32.028)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_4.um.cif, chain
spo11aa (#11) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_4.um.cif,
chain spo11aa (#5), sequence alignment score = 2071.6  
RMSD between 330 pruned atom pairs is 0.540 angstroms; (across all 425 pairs:
33.170)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_4.um.cif, chain
spo11aa (#11) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_0.um.cif,
chain spo11aa (#7), sequence alignment score = 2036.8  
RMSD between 331 pruned atom pairs is 0.437 angstroms; (across all 425 pairs:
37.251)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_4.um.cif, chain
spo11aa (#11) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_2.um.cif,
chain spo11aa (#9), sequence alignment score = 2051.2  
RMSD between 338 pruned atom pairs is 0.444 angstroms; (across all 425 pairs:
10.218)  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_4.um.cif, chain
spo11aa (#11) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2b_model_3.um.cif,
chain spo11aa (#10), sequence alignment score = 2031.4  
RMSD between 308 pruned atom pairs is 0.504 angstroms; (across all 425 pairs:
28.904)  
  

> save /Users/pcarlton/Desktop/k00session.cxs

——— End of log from Mon Jan 12 07:35:42 2026 ———

> view name session-start

opened ChimeraX session  

> close #2-5,7-31

> select add #1

33553 atoms, 34141 bonds, 193 pseudobonds, 1984 residues, 3 models selected  

> select subtract #1

1 model selected  

> select clear

[Repeated 1 time(s)]

> select /A,B

Nothing selected  

> info chains

chain id /spo11aa chain_id spo11aa  
chain id /spo11bb chain_id spo11bb  
chain id /dsb1X chain_id dsb1X  
chain id /dsb2 chain_id dsb2  
chain id /E chain_id E  
chain id /J chain_id J  
chain id /K chain_id K  
chain id /L chain_id L  

> ui tool show Log

> select /spo11aa,spo11bb

13685 atoms, 13815 bonds, 103 pseudobonds, 850 residues, 2 models selected  

> sequence chain #1/spo11aa,spo11bb

Alignment identifier is 1  

> select /spo11aa-spo11bb:49

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

> select /spo11aa-spo11bb:49-57

302 atoms, 302 bonds, 18 residues, 1 model selected  

> show sel atoms

> hide sel cartoons

> color sel byhetero

> style sel ball

Changed 302 atom styles  

> select clear

> sequence chain #1/spo11aa,spo11bb

Alignment identifier is 1  

> sequence chain #1/dsb1X

Alignment identifier is 1/dsb1X  

> sequence chain #1/dsb2

Alignment identifier is 1/dsb2  

> sequence chain #1/E

Alignment identifier is 1/E  

> sequence chain #1/J

Alignment identifier is 1/J  

> sequence chain #1/K

Alignment identifier is 1/K  

> sequence chain #1/L

Alignment identifier is 1/L  

> select /spo11aa-spo11bb:49

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

> select /spo11aa-spo11bb:49

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

> select /spo11aa-spo11bb:54

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select /spo11aa-spo11bb:54-55

58 atoms, 56 bonds, 4 residues, 1 model selected  

> select /spo11aa-spo11bb:54-55

58 atoms, 56 bonds, 4 residues, 1 model selected  

> select /spo11aa-spo11bb:54-55

58 atoms, 56 bonds, 4 residues, 1 model selected  

> select /spo11aa-spo11bb:56-57

44 atoms, 42 bonds, 4 residues, 1 model selected  

> select /spo11aa-spo11bb:56-57

44 atoms, 42 bonds, 4 residues, 1 model selected  

> select /spo11aa-spo11bb:54

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select /spo11aa-spo11bb:54

20 atoms, 18 bonds, 2 residues, 1 model selected  

> select /spo11aa:49@C

1 atom, 1 residue, 1 model selected  

> select up

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

> view sel

> select clear

> show atoms

> hide cartoons

> select clear

> color byhetero

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

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

> color sel yellow

> color sel byhetero

> ui tool show Rotamers

Populating font family aliases took 337 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

> swapaa interactive sel ALA rotLib Dunbrack

No rotamers for ALA in Dunbrack rotamer library  

> swapaa interactive sel ALA rotLib Dynameomics

No rotamers for ALA in Dynameomics rotamer library  

> ui tool show "Build Structure"

> delete atoms sel

> delete bonds sel

> select /spo11aa:49@CG

1 atom, 1 residue, 1 model selected  

> select up

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

> select down

1 atom, 1 residue, 1 model selected  

> select /spo11aa:49@CB

1 atom, 1 residue, 1 model selected  

> build modify /spo11aa:49@CB C 4 geometry tetrahedral resName ALA

> delete atoms sel

> delete bonds sel

> select /spo11aa:49@CG

1 atom, 1 residue, 1 model selected  

> select add /spo11aa:49@HG3

2 atoms, 1 residue, 1 model selected  

> select add /spo11aa:49@CD

3 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@HD3

4 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@HD2

5 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@NE

6 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@CZ

7 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@NH2

8 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@NH1

9 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@HH11

10 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@HH22

11 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@HH21

12 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@HH12

13 atoms, 1 bond, 1 residue, 1 model selected  

> select add /spo11aa:49@HE

14 atoms, 1 bond, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /spo11aa:49@CB

1 atom, 1 residue, 1 model selected  

> build modify /spo11aa:49@CB C 4 geometry tetrahedral

> select clear

[Repeated 1 time(s)]

> select /spo11aa:49@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> sequence chain #1/spo11aa

Alignment identifier is 1/spo11aa  

> select /spo11aa:52

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

> select /spo11aa:52

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

> swapaa /spo11aa,spo11bb:52 ALA

Using Dunbrack library  
Swapping /spo11aa GLU 52 to ALA  
Swapping /spo11bb GLU 52 to ALA  

> swapaa /spo11aa,spo11bb:53 ALA

Using Dunbrack library  
Swapping /spo11aa PHE 53 to ALA  
Swapping /spo11bb PHE 53 to ALA  

> swapaa /spo11aa,spo11bb:49 ALA

Using Dunbrack library  
Swapping /spo11aa ALA 49 to ALA  
Swapping /spo11bb ARG 49 to ALA  

> select clear

[Repeated 2 time(s)]

> view

> select clear

> hide atoms

> show cartoons

> select /spo11aa:49

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

> view sel

> select clear

> view

> select /spo11aa:49

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

> cofr sel

> select /spo11aa:49,53,54

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

> sequence chain #1/spo11aa

Destroying pre-existing alignment with identifier 1/spo11aa  
Alignment identifier is 1/spo11aa  

> select /spo11aa:49,52,53

15 atoms, 13 bonds, 3 residues, 1 model selected  

> show sel atoms

> contacts /spo1aa restrict /dsb1X select true reveal true log true

No atoms match given atom specifier  

> contacts /spo11aa restrict /dsb1X select true reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    106 contacts
           atom1                 atom2         overlap  distance
    /spo11aa ALA 53 CB    /dsb1X TYR 104 OH     0.376    3.004
    /spo11aa ILE 73 O     /dsb1X TYR 104 HE2    0.175    2.305
    /spo11aa GLU 39 O     /dsb1X TYR 62 HD2     0.133    2.347
    /spo11aa ALA 86 O     /dsb1X TYR 125 HE1    0.129    2.351
    /spo11aa ALA 52 CB    /dsb1X GLU 107 O      0.087    3.273
    /spo11aa ALA 52 CB    /dsb1X SER 106 HB2    0.083    2.797
    /spo11aa GLU 39 O     /dsb1X TYR 62 CD2     0.076    3.104
    /spo11aa ALA 86 O     /dsb1X TYR 125 CE1    0.074    3.106
    /spo11aa ASP 93 OD1   /dsb1X THR 121 CB     0.038    3.142
    /spo11aa ILE 73 O     /dsb1X TYR 104 CE2    0.036    3.144
    /spo11aa THR 85 C     /dsb1X TRP 124 HH2    0.030    2.670
    /spo11aa LEU 96 CB    /dsb1X SER 117 HG     0.022    2.678
    /spo11aa GLU 39 C     /dsb1X TYR 62 HD2     0.014    2.686
    /spo11aa GLN 46 NE2   /dsb1X SER 60 CB      0.001    3.324
    /spo11aa ILE 41 HD12  /dsb1X VAL 59 O       -0.035    2.515
    /spo11aa THR 85 O     /dsb1X TRP 124 HH2    -0.037    2.517
    /spo11aa GLU 107 CD   /dsb1X LYS 111 HZ1    -0.050    2.750
    /spo11aa ASP 93 OD1   /dsb1X THR 121 CG2    -0.070    3.250
    /spo11aa ASP 93 OD1   /dsb1X THR 121 HG21   -0.073    2.553
    /spo11aa ALA 53 CB    /dsb1X TYR 104 HH     -0.085    2.965
    /spo11aa ASP 38 O     /dsb1X TYR 62 CD2     -0.096    3.276
    /spo11aa HIS 100 CG   /dsb1X ARG 116 CD     -0.102    3.502
    /spo11aa ALA 53 CB    /dsb1X TYR 104 CZ     -0.121    3.701
    /spo11aa ASP 104 CG   /dsb1X ARG 116 NH2    -0.124    3.449
    /spo11aa LEU 96 HB3   /dsb1X SER 117 HG     -0.139    2.139
    /spo11aa ALA 56 CB    /dsb1X GLU 107 HB2    -0.140    2.840
    /spo11aa THR 85 C     /dsb1X TRP 124 CH2    -0.140    3.540
    /spo11aa THR 85 O     /dsb1X TRP 124 CH2    -0.152    3.332
    /spo11aa GLU 39 C     /dsb1X TYR 62 CD2     -0.162    3.562
    /spo11aa ILE 41 HG12  /dsb1X TYR 62 CZ      -0.164    2.864
    /spo11aa MET 62 SD    /dsb1X ASN 120 HB3    -0.169    2.951
    /spo11aa LEU 92 CD2   /dsb1X TRP 124 CZ3    -0.170    3.570
    /spo11aa GLU 107 CD   /dsb1X LYS 111 NZ     -0.175    3.500
    /spo11aa LEU 69 HG    /dsb1X TRP 124 CZ2    -0.177    2.877
    /spo11aa HIS 100 HB3  /dsb1X ARG 116 HH11   -0.179    2.179
    /spo11aa HIS 100 CD2  /dsb1X ARG 116 HD3    -0.179    2.879
    /spo11aa ALA 52 CB    /dsb1X SER 106 CB     -0.180    3.760
    /spo11aa LYS 50 HA    /dsb1X TYR 104 OH     -0.184    2.684
    /spo11aa ASP 93 OD1   /dsb1X THR 121 OG1    -0.188    2.768
    /spo11aa ILE 41 HG12  /dsb1X TYR 62 CE2     -0.189    2.889
    /spo11aa ASP 104 OD2  /dsb1X ARG 116 CZ     -0.196    3.376
    /spo11aa LYS 89 HD2   /dsb1X TYR 125 CG     -0.197    2.897
    /spo11aa ASP 38 O     /dsb1X TYR 62 CE2     -0.198    3.378
    /spo11aa GLU 107 OE2  /dsb1X LYS 111 CE     -0.200    3.380
    /spo11aa HIS 100 CB   /dsb1X ARG 116 HD2    -0.205    2.905
    /spo11aa ALA 52 CB    /dsb1X GLU 107 H      -0.205    3.085
    /spo11aa HIS 100 HB3  /dsb1X ARG 116 NH1    -0.215    2.840
    /spo11aa HIS 100 CB   /dsb1X ARG 116 CD     -0.216    3.616
    /spo11aa ILE 41 CD1   /dsb1X VAL 59 O       -0.221    3.401
    /spo11aa ILE 41 HD11  /dsb1X ARG 61 O       -0.224    2.704
    /spo11aa GLN 46 CD    /dsb1X SER 60 CB      -0.237    3.637
    /spo11aa LEU 96 CB    /dsb1X SER 117 OG     -0.238    3.438
    /spo11aa GLN 46 NE2   /dsb1X SER 60 HB2     -0.239    2.864
    /spo11aa ASP 104 OD1  /dsb1X ARG 116 HH22   -0.241    2.321
    /spo11aa ASP 104 CG   /dsb1X ARG 116 HH22   -0.245    2.945
    /spo11aa HIS 100 CD2  /dsb1X ARG 116 CD     -0.249    3.649
    /spo11aa GLU 107 OE1  /dsb1X LYS 111 CE     -0.251    3.431
    /spo11aa ASP 104 CG   /dsb1X ARG 116 NH1    -0.254    3.579
    /spo11aa HIS 100 CE1  /dsb1X ARG 116 HB3    -0.257    2.957
    /spo11aa HIS 100 HB3  /dsb1X ARG 116 HD2    -0.259    2.259
    /spo11aa LYS 89 HZ1   /dsb1X ASP 122 OD1    -0.259    2.339
    /spo11aa HIS 100 HB3  /dsb1X ARG 116 CD     -0.260    2.960
    /spo11aa HIS 100 CB   /dsb1X ARG 116 HH11   -0.264    2.964
    /spo11aa HIS 100 HE1  /dsb1X SER 117 HB3    -0.264    2.264
    /spo11aa THR 75 OG1   /dsb1X MET 57 CE      -0.269    3.469
    /spo11aa ASP 104 OD1  /dsb1X ARG 116 CZ     -0.273    3.453
    /spo11aa LEU 96 HB3   /dsb1X SER 117 CB     -0.278    2.978
    /spo11aa ALA 56 CB    /dsb1X GLU 107 CB     -0.282    3.682
    /spo11aa ASP 38 O     /dsb1X TYR 62 HD2     -0.283    2.763
    /spo11aa ILE 73 O     /dsb1X TYR 104 HH     -0.285    2.365
    /spo11aa MET 62 HA    /dsb1X TRP 124 CD1    -0.293    2.993
    /spo11aa GLU 66 O     /dsb1X TRP 124 HE1    -0.294    2.374
    /spo11aa GLU 107 OE1  /dsb1X LYS 111 HE2    -0.305    2.785
    /spo11aa ASP 104 OD1  /dsb1X ARG 116 NH2    -0.309    3.014
    /spo11aa LYS 89 HD2   /dsb1X TYR 125 CD1    -0.310    3.010
    /spo11aa GLU 39 O     /dsb1X TYR 62 H       -0.314    2.394
    /spo11aa MET 62 SD    /dsb1X ASN 120 CB     -0.326    3.808
    /spo11aa ALA 86 O     /dsb1X TYR 125 CD1    -0.329    3.509
    /spo11aa LEU 69 CG    /dsb1X TRP 124 CZ2    -0.331    3.731
    /spo11aa LEU 96 CB    /dsb1X SER 117 CB     -0.335    3.735
    /spo11aa HIS 100 CD2  /dsb1X ARG 116 HH11   -0.336    3.036
    /spo11aa HIS 100 CG   /dsb1X ARG 116 HD3    -0.338    3.038
    /spo11aa LEU 96 HB3   /dsb1X SER 117 OG     -0.338    2.838
    /spo11aa GLN 46 NE2   /dsb1X SER 60 CA      -0.339    3.664
    /spo11aa GLU 39 CA    /dsb1X TYR 62 HD2     -0.340    3.040
    /spo11aa ALA 56 HB2   /dsb1X GLU 107 HB2    -0.340    2.340
    /spo11aa LYS 89 CD    /dsb1X TYR 125 CG     -0.341    3.741
    /spo11aa ASP 104 OD1  /dsb1X ARG 116 HH12   -0.343    2.423
    /spo11aa GLU 107 CD   /dsb1X LYS 111 CE     -0.349    3.749
    /spo11aa LYS 50 HG3   /dsb1X VAL 59 HG11    -0.349    2.349
    /spo11aa ILE 41 CG1   /dsb1X TYR 62 CE2     -0.350    3.750
    /spo11aa ILE 41 HD11  /dsb1X ARG 61 C       -0.365    3.065
    /spo11aa HIS 100 ND1  /dsb1X ARG 116 CB     -0.366    3.691
    /spo11aa GLU 39 O     /dsb1X ARG 61 HA      -0.368    2.848
    /spo11aa ALA 86 C     /dsb1X TYR 125 HE1    -0.370    3.070
    /spo11aa HIS 100 CB   /dsb1X ARG 116 NH1    -0.376    3.701
    /spo11aa HIS 100 CE1  /dsb1X SER 117 HB3    -0.380    3.080
    /spo11aa HIS 100 CG   /dsb1X ARG 116 HD2    -0.384    3.084
    /spo11aa LEU 92 CD2   /dsb1X THR 121 HG22   -0.388    3.088
    /spo11aa MET 62 CE    /dsb1X THR 121 CG2    -0.389    3.789
    /spo11aa ASP 104 OD1  /dsb1X ARG 116 NH1    -0.390    3.095
    /spo11aa ASP 104 CG   /dsb1X ARG 116 HH12   -0.395    3.095
    /spo11aa HIS 100 CE1  /dsb1X ARG 116 CB     -0.395    3.795
    /spo11aa ALA 86 HB2   /dsb1X VAL 128 CG1    -0.396    3.096
    /spo11aa LYS 50 CG    /dsb1X VAL 59 HG11    -0.396    3.096
    /spo11aa ILE 41 CD1   /dsb1X ARG 61 O       -0.399    3.579
    

  
106 contacts  

> select clear

> save /Users/pcarlton/Desktop/spo11x2_3Abyhand_DSB123_splitDNA.pdb

Chain IDs longer than 2 characters; truncating  

> select clear

> open
> /Users/pcarlton/Desktop/af3/SPORM/k00cel/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif

Summary of feedback from opening
/Users/pcarlton/Desktop/af3/SPORM/k00cel/fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' on line 53  
Missing entity information. Treating each chain as a separate entity.  
Missing or incorrect sequence information. Inferred polymer connectivity.  
Skipping chem_comp category: Missing column 'type' on line 33678  
  
Chain information for
fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2  
---  
Chain | Description  
A B | No description available  
C | No description available  
D | No description available  
E | No description available  
J | No description available  
K | No description available  
L | No description available  
  

> hide atoms

> show ribbons

Computing secondary structure  

> info chains

chain id #1/spo11aa chain_id spo11aa  
chain id #1/spo11bb chain_id spo11bb  
chain id #1/dsb1X chain_id dsb1X  
chain id #1/dsb2 chain_id dsb2  
chain id #1/E chain_id E  
chain id #1/J chain_id J  
chain id #1/K chain_id K  
chain id #1/L chain_id L  
chain id #2/A chain_id A  
chain id #2/B chain_id B  
chain id #2/C chain_id C  
chain id #2/D chain_id D  
chain id #2/E chain_id E  
chain id #2/J chain_id J  
chain id #2/K chain_id K  
chain id #2/L chain_id L  

> mmaker #1/spo11aa to #2/A

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif, chain A
(#2) with fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif, chain
spo11aa (#1), sequence alignment score = 2163.2  
RMSD between 425 pruned atom pairs is 0.000 angstroms; (across all 425 pairs:
0.000)  
  

> select clear

> color bychain

> select /spo11aa,A

13644 atoms, 13773 bonds, 850 residues, 2 models selected  

> select /spo11aa,A:48-55

248 atoms, 247 bonds, 16 residues, 2 models selected  

> view sel

> show sel atoms

> color sel byhetero

> style sel ball

Changed 248 atom styles  

> ui tool show "Side View"

> save /Users/pcarlton/Desktop/3A-work.cxs

> select /spo11aa:49,53,54

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

> select /spo11aa:49,52,53

15 atoms, 13 bonds, 3 residues, 1 model selected  

> color sel yellow

> style sel ball

Changed 15 atom styles  

> color sel byhetero

> select /A:49,52,53

59 atoms, 58 bonds, 3 residues, 1 model selected  

> contacts sel restrict /C log true reveal true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    38 contacts
                                      atom1                                                                       atom2                                     overlap  distance
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 OH    0.209    2.991
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 HD1   0.154    2.471
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 HD2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C ILE 105 O     0.112    2.368
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CD    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 OG     0.003    3.197
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 HD2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 OG     -0.006    2.506
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CD2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C ILE 105 O     -0.025    3.205
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 CD1   -0.030    3.355
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LEU 65 H      -0.041    2.666
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 HB3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 O     -0.050    2.530
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LYS 66 CE     -0.070    3.250
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CZ    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 HA     -0.074    2.774
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 HB3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 OH    -0.077    2.577
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 HA     -0.086    2.711
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 O     -0.100    3.280
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 CB    -0.110    3.290
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LEU 65 N      -0.144    3.394
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 HB2   -0.152    2.852
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 HB2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 OH    -0.159    2.659
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LYS 66 NZ     -0.182    2.887
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 HB3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 H     -0.192    2.192
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CZ    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 OG     -0.194    3.394
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CZ    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 CA     -0.196    3.596
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LYS 66 HE3    -0.219    2.699
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 HH21  fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 HD1   -0.237    2.237
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 O     -0.245    3.425
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 HH    -0.271    2.971
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 CZ    -0.274    3.674
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 CA     -0.277    3.602
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 HG    -0.290    2.370
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 HB2   -0.296    2.776
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 HD2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 HG     -0.302    2.302
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 OG    -0.307    2.887
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LYS 66 HZ2    -0.313    2.393
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 OH    -0.323    3.523
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 HA     -0.335    2.960
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NE    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 OG     -0.337    3.062
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CZ    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 CB     -0.374    3.774
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 HG2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 O     -0.385    2.865
    

  
38 contacts  

> contacts sel restrict /C log true reveal true select true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: True
    
    38 contacts
                                      atom1                                                                       atom2                                     overlap  distance
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 OH    0.209    2.991
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 HD1   0.154    2.471
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 HD2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C ILE 105 O     0.112    2.368
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CD    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 OG     0.003    3.197
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 HD2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 OG     -0.006    2.506
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CD2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C ILE 105 O     -0.025    3.205
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 CD1   -0.030    3.355
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LEU 65 H      -0.041    2.666
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 HB3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 O     -0.050    2.530
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LYS 66 CE     -0.070    3.250
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CZ    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 HA     -0.074    2.774
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 HB3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 OH    -0.077    2.577
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 HA     -0.086    2.711
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 O     -0.100    3.280
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 CB    -0.110    3.290
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LEU 65 N      -0.144    3.394
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 HB2   -0.152    2.852
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 HB2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 OH    -0.159    2.659
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LYS 66 NZ     -0.182    2.887
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 HB3   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 H     -0.192    2.192
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CZ    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 OG     -0.194    3.394
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CZ    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 CA     -0.196    3.596
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LYS 66 HE3    -0.219    2.699
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 HH21  fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 HD1   -0.237    2.237
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 O     -0.245    3.425
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 HH    -0.271    2.971
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CB    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 CZ    -0.274    3.674
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 CA     -0.277    3.602
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 HG    -0.290    2.370
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 HB2   -0.296    2.776
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 HD2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 HG     -0.302    2.302
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 106 OG    -0.307    2.887
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 OE2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C LYS 66 HZ2    -0.313    2.393
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A PHE 53 CG    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C TYR 104 OH    -0.323    3.523
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NH1   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 HA     -0.335    2.960
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 NE    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 OG     -0.337    3.062
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A ARG 49 CZ    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C SER 64 CB     -0.374    3.774
    fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/A GLU 52 HG2   fold_k00cele_spo_11x2_dsb123_mg4_splitdna2_model_0.um.cif #2/C GLU 107 O     -0.385    2.865
    

  
38 contacts  

> style sel ball

Changed 42 atom styles  

> select up

177 atoms, 175 bonds, 10 residues, 1 model selected  

> style sel ball

Changed 177 atom styles  

> color sel byhetero

> select clear

> save /Users/pcarlton/Desktop/3A-work.cxs

——— End of log from Wed Jan 28 16:58:23 2026 ———

> view name session-start

opened ChimeraX session  

> ui tool show "Find Cavities"

> select /spo11aa:45-55

144 atoms, 143 bonds, 11 residues, 1 model selected  

> kvfinder #1 boxAtoms sel

> open /var/folders/25/zlmkhzy16_xbfsfgb5y03b_h0000gn/T/tmph6drunc9.bild id
> 1.5 name "cavity search box"

Opened BILD data containing 15 objects  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 131, in <lambda>  
bbox.button(qbbox.Apply).clicked.connect(lambda *args, fc=self.find_cavities:
fc(apply=True))  
^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/tool.py", line 172, in find_cavities  
run(self.session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/cmd.py", line 73, in cmd_kvfinder  
struct_input, vertices = prep_input(s, include_atoms, box_origin, box_extent,
show_box,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/prep.py", line 90, in prep_input  
from _pyKVFinder import _filter_pdb  
ModuleNotFoundError: No module named '_pyKVFinder'  
  
ModuleNotFoundError: No module named '_pyKVFinder'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/kvfinder/prep.py", line 90, in prep_input  
from _pyKVFinder import _filter_pdb  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac15,13
      Model Number: MXD33J/A
      Chip: Apple M3
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.140.96
      OS Loader Version: 11881.140.96

Software:

    System Software Overview:

      System Version: macOS 15.6 (24G84)
      Kernel Version: Darwin 24.6.0
      Time since boot: 13 days, 10 hours, 8 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2880 x 1864 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.1
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.2
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.63.0
    ChimeraX-AtomicLibrary: 14.2.3
    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: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    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: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12.dev202601270036
    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: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.8.1
    ChimeraX-Label: 1.3
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.4
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.12
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.5
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.7
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.4
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.2
    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: 1.50.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.2
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.15.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 2.4.1
    numpy: 1.26.4
    OpenMM: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    plotly: 6.5.2
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.9.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.1
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.1
    PyQt6_sip: 13.10.3
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.22
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.3
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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
    sse-starlette: 3.2.0
    stack-data: 0.6.3
    starlette: 0.52.1
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.14.0
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    urllib3: 2.6.3
    uvicorn: 0.40.0
    wcwidth: 0.5.0
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0

Change History (2)

comment:1 by Eric Pettersen, 25 hours ago

Component:	Unassigned → Surface/Binding Analysis
Description:	modified (diff)
Owner:	set to Eric Pettersen
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → kvfinder fails with "boxAtoms" option

comment:2 by Eric Pettersen, 22 hours ago

Resolution:	→ fixed
Status:	accepted → closed

Hi Peter,

Thanks for reporting this problem. It seems the newest version of pyKVFinder changed the location of a submodule, which broke the ChimeraX interface to it. Fixed in tomorrow's daily build.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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