zonesel: NumPy array is not contiguous

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.0-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/ALPHAFOLD_IDRIS/AF_scRad50_rif2bat/analyse_CFcomp.cxc
> format cmd

> open ranked_0.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/cutting_state/NAMD/cutting_traj_frame_state08.pdb
> segidChains true

Chain information for cutting_traj_frame_state08.pdb #2  
---  
Chain | Description  
DNAE | No description available  
DNAF | No description available  
MREA MREB | No description available  
RADC RADD | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/resting_state/NAMD/rad50_mre11_sc_dynawat_traj__state010.pdb
> segidChains true

Chain information for rad50_mre11_sc_dynawat_traj__state010.pdb #3  
---  
Chain | Description  
MREC MRED | No description available  
RADA RADB | No description available  
  

> open 7ZR1

7zr1 title:  
Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite
structure) [more info...]  
  
Chain information for 7zr1 #4  
---  
Chain | Description | UniProt  
A B | Double-strand break repair protein | G0RYR3_CHATD  
C D | DH domain-containing protein | G0SHW7_CHATD  
E | FHA domain-containing protein | G0SAV1_CHATD  
  
Non-standard residues in 7zr1 #4  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
MN — manganese (II) ion  
  

> rename #2 scRap1_mre11_cutting_state

> rename #3 scRap1_mre11_resting_state

> mmaker #2 to #1

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 ranked_0.pdb, chain A (#1) with scRap1_mre11_cutting_state, chain
RADD (#2), sequence alignment score = 1810.4  
RMSD between 246 pruned atom pairs is 1.011 angstroms; (across all 382 pairs:
3.440)  
  

> mmaker #3 to #1

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 ranked_0.pdb, chain A (#1) with scRap1_mre11_resting_state, chain
RADB (#3), sequence alignment score = 1756.4  
RMSD between 197 pruned atom pairs is 1.018 angstroms; (across all 382 pairs:
3.915)  
  

> mmaker #4 to #1

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 ranked_0.pdb, chain A (#1) with 7zr1, chain C (#4), sequence
alignment score = 630.2  
RMSD between 159 pruned atom pairs is 0.963 angstroms; (across all 297 pairs:
89.814)  
  

> select all

81731 atoms, 82714 bonds, 31 pseudobonds, 6472 residues, 6 models selected  

> hide sel target a

> show sel target c

> graphics silhouettes true

> lighting soft

> set bgColor white

executed analyse_CFcomp.cxc  

> select subtract #1

74616 atoms, 75544 bonds, 31 pseudobonds, 6030 residues, 5 models selected  

> select subtract #2

47161 atoms, 47758 bonds, 31 pseudobonds, 4288 residues, 4 models selected  

> select subtract #3

21793 atoms, 22130 bonds, 31 pseudobonds, 2694 residues, 3 models selected  

> hide #2 models

> hide #3 models

> select clear

> hide #1 models

> show #1 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> hide #!4 models

> show #!4 models

> hide #1 models

> hide #!4 models

> show #3 models

> show #!4 models

> hide #!4 models

> show #1 models

> hide #3 models

> delete *

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete all

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/ALPHAFOLD_IDRIS/AF_scRad50_rif2bat/analyse_CFcomp.cxc

> open ranked_0.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/cutting_state/NAMD/cutting_traj_frame_state08.pdb
> segidChains true

Chain information for cutting_traj_frame_state08.pdb #2  
---  
Chain | Description  
DNAE | No description available  
DNAF | No description available  
MREA MREB | No description available  
RADC RADD | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/resting_state/NAMD/rad50_mre11_sc_dynawat_traj__state010.pdb
> segidChains true

Chain information for rad50_mre11_sc_dynawat_traj__state010.pdb #3  
---  
Chain | Description  
MREC MRED | No description available  
RADA RADB | No description available  
  

> open 7ZR1

7zr1 title:  
Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite
structure) [more info...]  
  
Chain information for 7zr1 #4  
---  
Chain | Description | UniProt  
A B | Double-strand break repair protein | G0RYR3_CHATD  
C D | DH domain-containing protein | G0SHW7_CHATD  
E | FHA domain-containing protein | G0SAV1_CHATD  
  
Non-standard residues in 7zr1 #4  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
MN — manganese (II) ion  
  

> rename #2 scRap1_mre11_cutting_state

> rename #3 scRap1_mre11_resting_state

> mmaker #2/MREC/MRED to #4/C/D

No molecules/chains to match specified  

> hide #1 models

> hide #3 models

> hide #!4 models

> view #2

> hide #2 target a

> show #2 target c

> delete all

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/ALPHAFOLD_IDRIS/AF_scRad50_rif2bat/analyse_CFcomp.cxc

> open ranked_0.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/cutting_state/NAMD/cutting_traj_frame_state08.pdb
> segidChains true

Chain information for cutting_traj_frame_state08.pdb #2  
---  
Chain | Description  
DNAE | No description available  
DNAF | No description available  
MREA MREB | No description available  
RADC RADD | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/resting_state/NAMD/rad50_mre11_sc_dynawat_traj__state010.pdb
> segidChains true

Chain information for rad50_mre11_sc_dynawat_traj__state010.pdb #3  
---  
Chain | Description  
MREC MRED | No description available  
RADA RADB | No description available  
  

> open 7ZR1

7zr1 title:  
Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite
structure) [more info...]  
  
Chain information for 7zr1 #4  
---  
Chain | Description | UniProt  
A B | Double-strand break repair protein | G0RYR3_CHATD  
C D | DH domain-containing protein | G0SHW7_CHATD  
E | FHA domain-containing protein | G0SAV1_CHATD  
  
Non-standard residues in 7zr1 #4  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
MN — manganese (II) ion  
  

> rename #2 scRap1_mre11_cutting_state

> rename #3 scRap1_mre11_resting_state

> mmaker #2/MREA/MREB to #4/C/D

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 7zr1, chain C (#4) with scRap1_mre11_cutting_state, chain MREA
(#2), sequence alignment score = 55.2  
RMSD between 14 pruned atom pairs is 1.331 angstroms; (across all 117 pairs:
17.158)  
  

> mmaker #3/MREC/MRED to #4/C/D

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 7zr1, chain C (#4) with scRap1_mre11_resting_state, chain MREC
(#3), sequence alignment score = 63.1  
RMSD between 13 pruned atom pairs is 1.377 angstroms; (across all 120 pairs:
17.552)  
  

> mmaker #1/A to #4/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 7zr1, chain A (#4) with ranked_0.pdb, chain A (#1), sequence
alignment score = 27  
RMSD between 14 pruned atom pairs is 1.229 angstroms; (across all 110 pairs:
16.963)  
  

> select all

81731 atoms, 82714 bonds, 31 pseudobonds, 6472 residues, 6 models selected  

> hide sel target a

> show sel target c

> graphics silhouettes true

> lighting soft

> set bgColor white

> color #1/B red

> color #1/A wheat

> color #4/A pale green

> color #4/B lignt blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> delete all

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/SMC_condensin/modeller/scSMC4/CHARMM/s4aA.pdb
> format pdb

Chain information for s4aA.pdb #1  
---  
Chain | Description  
A | No description available  
  

> delete all

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/ALPHAFOLD_IDRIS/AF_scRad50_rif2bat/analyse_CFcomp.cxc

> open ranked_0.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/cutting_state/NAMD/cutting_traj_frame_state08.pdb
> segidChains true

Chain information for cutting_traj_frame_state08.pdb #2  
---  
Chain | Description  
DNAE | No description available  
DNAF | No description available  
MREA MREB | No description available  
RADC RADD | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/resting_state/NAMD/rad50_mre11_sc_dynawat_traj__state010.pdb
> segidChains true

Chain information for rad50_mre11_sc_dynawat_traj__state010.pdb #3  
---  
Chain | Description  
MREC MRED | No description available  
RADA RADB | No description available  
  

> open 7ZR1

7zr1 title:  
Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite
structure) [more info...]  
  
Chain information for 7zr1 #4  
---  
Chain | Description | UniProt  
A B | Double-strand break repair protein | G0RYR3_CHATD  
C D | DH domain-containing protein | G0SHW7_CHATD  
E | FHA domain-containing protein | G0SAV1_CHATD  
  
Non-standard residues in 7zr1 #4  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
MN — manganese (II) ion  
  

> rename #2 scRap1_mre11_cutting_state

> rename #3 scRap1_mre11_resting_state

> mmaker #2/MREA/MREB to #4/C/D

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 7zr1, chain C (#4) with scRap1_mre11_cutting_state, chain MREA
(#2), sequence alignment score = 55.2  
RMSD between 14 pruned atom pairs is 1.331 angstroms; (across all 117 pairs:
17.158)  
  

> mmaker #3/MREC/MRED to #4/C/D

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 7zr1, chain C (#4) with scRap1_mre11_resting_state, chain MREC
(#3), sequence alignment score = 63.1  
RMSD between 13 pruned atom pairs is 1.377 angstroms; (across all 120 pairs:
17.552)  
  

> mmaker #1/A to #4/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 7zr1, chain A (#4) with ranked_0.pdb, chain A (#1), sequence
alignment score = 27  
RMSD between 14 pruned atom pairs is 1.229 angstroms; (across all 110 pairs:
16.963)  
  

> select all

81731 atoms, 82714 bonds, 31 pseudobonds, 6472 residues, 6 models selected  

> hide sel target a

> show sel target c

> graphics silhouettes true

> lighting soft

> set bgColor white

> color #1/B red

> color #1/A wheat

> color #4/A pale green

> color #4/B light blue

> color #4/C orange

> color #4/D khaki

> color #3/MREC lignt blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> delete all

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/ALPHAFOLD_IDRIS/AF_scRad50_rif2bat/analyse_CFcomp.cxc

> open ranked_0.pdb

Chain information for ranked_0.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/cutting_state/NAMD/cutting_traj_frame_state08.pdb
> segidChains true

Chain information for cutting_traj_frame_state08.pdb #2  
---  
Chain | Description  
DNAE | No description available  
DNAF | No description available  
MREA MREB | No description available  
RADC RADD | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/resting_state/NAMD/rad50_mre11_sc_dynawat_traj__state010.pdb
> segidChains true

Chain information for rad50_mre11_sc_dynawat_traj__state010.pdb #3  
---  
Chain | Description  
MREC MRED | No description available  
RADA RADB | No description available  
  

> open 7ZR1

7zr1 title:  
Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite
structure) [more info...]  
  
Chain information for 7zr1 #4  
---  
Chain | Description | UniProt  
A B | Double-strand break repair protein | G0RYR3_CHATD  
C D | DH domain-containing protein | G0SHW7_CHATD  
E | FHA domain-containing protein | G0SAV1_CHATD  
  
Non-standard residues in 7zr1 #4  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
MN — manganese (II) ion  
  

> rename #2 scRap1_mre11_cutting_state

> rename #3 scRap1_mre11_resting_state

> mmaker #2/MREA/MREB to #4/C/D

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 7zr1, chain C (#4) with scRap1_mre11_cutting_state, chain MREA
(#2), sequence alignment score = 55.2  
RMSD between 14 pruned atom pairs is 1.331 angstroms; (across all 117 pairs:
17.158)  
  

> mmaker #3/MREC/MRED to #4/C/D

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 7zr1, chain C (#4) with scRap1_mre11_resting_state, chain MREC
(#3), sequence alignment score = 63.1  
RMSD between 13 pruned atom pairs is 1.377 angstroms; (across all 120 pairs:
17.552)  
  

> mmaker #1/A to #4/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 7zr1, chain A (#4) with ranked_0.pdb, chain A (#1), sequence
alignment score = 27  
RMSD between 14 pruned atom pairs is 1.229 angstroms; (across all 110 pairs:
16.963)  
  

> select all

81731 atoms, 82714 bonds, 31 pseudobonds, 6472 residues, 6 models selected  

> hide sel target a

> show sel target c

> graphics silhouettes true

> lighting soft

> set bgColor white

> color #1/B red

> color #1/A wheat

> color #4/A pale green

> color #4/B light blue

> color #4/C orange

> color #4/D khaki

> color #3/MREC light blue

> color #3/MRED pale green

executed analyse_CFcomp.cxc  

> view #3

> hide #3 models

> hide #2 models

> hide #1 models

> select clear

> show #1 models

> delete all

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/ALPHAFOLD_IDRIS/AF_scRad50_rif2bat/analyse_CFcomp.cxc

> open ranked_0.pdb name 1_AF2_scRad50_Bat_ranked_0

Chain information for 1_AF2_scRad50_Bat_ranked_0 #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/cutting_state/NAMD/cutting_traj_frame_state08.pdb
> segidChains true

Chain information for cutting_traj_frame_state08.pdb #2  
---  
Chain | Description  
DNAE | No description available  
DNAF | No description available  
MREA MREB | No description available  
RADC RADD | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/resting_state/NAMD/rad50_mre11_sc_dynawat_traj__state010.pdb
> segidChains true

Chain information for rad50_mre11_sc_dynawat_traj__state010.pdb #3  
---  
Chain | Description  
MREC MRED | No description available  
RADA RADB | No description available  
  

> open 7ZR1

7zr1 title:  
Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite
structure) [more info...]  
  
Chain information for 7zr1 #4  
---  
Chain | Description | UniProt  
A B | Double-strand break repair protein | G0RYR3_CHATD  
C D | DH domain-containing protein | G0SHW7_CHATD  
E | FHA domain-containing protein | G0SAV1_CHATD  
  
Non-standard residues in 7zr1 #4  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
MN — manganese (II) ion  
  

> open ranked_0.pdb name 2_AF2_scRad50_Bat_ranked_0

Chain information for 2_AF2_scRad50_Bat_ranked_0 #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> rename #2 scRap1_mre11_cutting_state

> rename #3 scRap1_mre11_resting_state

> mmaker #2/MREA/MREB to #4/C/D

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 7zr1, chain C (#4) with scRap1_mre11_cutting_state, chain MREA
(#2), sequence alignment score = 55.2  
RMSD between 14 pruned atom pairs is 1.331 angstroms; (across all 117 pairs:
17.158)  
  

> mmaker #3/MREC/MRED to #4/C/D

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 7zr1, chain C (#4) with scRap1_mre11_resting_state, chain MREC
(#3), sequence alignment score = 63.1  
RMSD between 13 pruned atom pairs is 1.377 angstroms; (across all 120 pairs:
17.552)  
  

> mmaker #1/A to #4/C

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7zr1, chain C (#4) with 1_AF2_scRad50_Bat_ranked_0, chain A (#1),
sequence alignment score = 645.6  
RMSD between 158 pruned atom pairs is 0.956 angstroms; (across all 297 pairs:
89.811)  
  

> mmaker #5/A to #4/D

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 7zr1, chain D (#4) with 2_AF2_scRad50_Bat_ranked_0, chain A (#5),
sequence alignment score = 649.4  
RMSD between 163 pruned atom pairs is 0.903 angstroms; (across all 297 pairs:
90.763)  
  

> select all

88846 atoms, 89884 bonds, 31 pseudobonds, 6914 residues, 7 models selected  

> hide sel target a

> show sel target c

> graphics silhouettes true

> lighting soft

> set bgColor white

> color #1/B red

> color #1/A wheat

> color #4/A pale green

> color #4/B light blue

> color #4/C orange

> color #4/D khaki

> color #3/MREC light blue

> color #3/MRED pale green

executed analyse_CFcomp.cxc  

> view clip false

> select clear

> hide #2 models

> hide #5 models

> show #5 models

> hide #5 models

> hide #1 models

> show #1 models

> hide #3 models

> show #5 models

> show #2 models

> hide #2 models

> show #3 models

> hide #3 models

> delete all

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/ALPHAFOLD_IDRIS/AF_scRad50_rif2bat/analyse_CFcomp.cxc

> open ranked_0.pdb name 1_AF2_scRad50_Bat_ranked_0

Chain information for 1_AF2_scRad50_Bat_ranked_0 #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/cutting_state/NAMD/cutting_traj_frame_state08.pdb
> segidChains true

Chain information for cutting_traj_frame_state08.pdb #2  
---  
Chain | Description  
DNAE | No description available  
DNAF | No description available  
MREA MREB | No description available  
RADC RADD | No description available  
  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/Modele_MRre11_Rad50_sc/resting_state/NAMD/rad50_mre11_sc_dynawat_traj__state010.pdb
> segidChains true

Chain information for rad50_mre11_sc_dynawat_traj__state010.pdb #3  
---  
Chain | Description  
MREC MRED | No description available  
RADA RADB | No description available  
  

> open 7ZR1

7zr1 title:  
Chaetomium thermophilum Mre11-Rad50-Nbs1 complex bound to ATPyS (composite
structure) [more info...]  
  
Chain information for 7zr1 #4  
---  
Chain | Description | UniProt  
A B | Double-strand break repair protein | G0RYR3_CHATD  
C D | DH domain-containing protein | G0SHW7_CHATD  
E | FHA domain-containing protein | G0SAV1_CHATD  
  
Non-standard residues in 7zr1 #4  
---  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
MN — manganese (II) ion  
  

> open ranked_0.pdb name 2_AF2_scRad50_Bat_ranked_0

Chain information for 2_AF2_scRad50_Bat_ranked_0 #5  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> rename #2 scRap1_mre11_cutting_state

> rename #3 scRap1_mre11_resting_state

> mmaker #2/MREA/MREB to #4/A/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 7zr1, chain A (#4) with scRap1_mre11_cutting_state, chain MREA
(#2), sequence alignment score = 1223.9  
RMSD between 267 pruned atom pairs is 1.086 angstroms; (across all 404 pairs:
3.540)  
  

> mmaker #3/MREC/MRED to #4/A/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 7zr1, chain A (#4) with scRap1_mre11_resting_state, chain MREC
(#3), sequence alignment score = 1226.2  
RMSD between 257 pruned atom pairs is 1.055 angstroms; (across all 404 pairs:
5.377)  
  

> mmaker #1/A to #4/C

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 7zr1, chain C (#4) with 1_AF2_scRad50_Bat_ranked_0, chain A (#1),
sequence alignment score = 645.6  
RMSD between 158 pruned atom pairs is 0.956 angstroms; (across all 297 pairs:
89.811)  
  

> mmaker #5/A to #4/D

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 7zr1, chain D (#4) with 2_AF2_scRad50_Bat_ranked_0, chain A (#5),
sequence alignment score = 649.4  
RMSD between 163 pruned atom pairs is 0.903 angstroms; (across all 297 pairs:
90.763)  
  

> select all

88846 atoms, 89884 bonds, 31 pseudobonds, 6914 residues, 7 models selected  

> hide sel target a

> show sel target c

> graphics silhouettes true

> lighting soft

> set bgColor white

> color #1/B red

> color #1/A wheat

> color #4/A pale green

> color #4/B light blue

> color #4/C orange

> color #4/D khaki

> color #3/MREC light blue

> color #3/MRED pale green

executed analyse_CFcomp.cxc  

> view #1 clip false

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> select clear

> hide #5 models

> hide #1 models

> hide #3 models

> show #3 models

> show #2 models

> hide #3 models

> show #1 models

> show #5 models

> hide #1 models

> hide #5 models

> hide #2 models

> show #3 models

> show #2 models

> hide #3 models

> hide #2 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> hide #!4 models

> show #!4 models

> show #2 models

> hide #2 models

> show #3 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #3 models

> mmaker #3/RADA/RADB to #4/C/D

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 7zr1, chain C (#4) with scRap1_mre11_resting_state, chain RADA
(#3), sequence alignment score = 562.1  
RMSD between 136 pruned atom pairs is 1.025 angstroms; (across all 295 pairs:
91.011)  
  

> show #3 models

> hide #3 models

> open 5DAC

Summary of feedback from opening 5DAC fetched from pdb  
---  
notes | Fetching compressed mmCIF 5dac from
http://files.rcsb.org/download/5dac.cif  
Fetching CCD AES from http://ligand-expo.rcsb.org/reports/A/AES/AES.cif  
  
5dac title:  
ATP-gamma-S bound Rad50 from Chaetomium thermophilum in complex with DNA [more
info...]  
  
Chain information for 5dac #6  
---  
Chain | Description | UniProt  
A B | Putative uncharacterized protein,Putative uncharacterized protein |
G0SHW7_CHATD  
C | DNA (5'-D(P*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*CP*C)-3') |  
D | DNA (5'-D(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3') |  
  
Non-standard residues in 5dac #6  
---  
AES — 4-(2-aminoethyl)benzenesulfonyl fluoride (AEBSF)  
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)  
MG — magnesium ion  
  

> hide #!4 models

> view 5dac

Expected an objects specifier or a view name or a keyword  

> view #6

> mmaker #6 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker scRap1_mre11_cutting_state, chain RADD (#2) with 5dac, chain A
(#6), sequence alignment score = 1159.4  
RMSD between 240 pruned atom pairs is 1.184 angstroms; (across all 376 pairs:
3.793)  
  

> view #2

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> open 6s85

Summary of feedback from opening 6s85 fetched from pdb  
---  
note | Fetching compressed mmCIF 6s85 from
http://files.rcsb.org/download/6s85.cif  
  
6s85 title:  
Cutting state of the E. coli Mre11-Rad50 (SbcCD) head complex bound to ADP and
dsDNA. [more info...]  
  
Chain information for 6s85 #7  
---  
Chain | Description | UniProt  
A B | Nuclease SbcCD subunit D | C3TMC7_ECOLX  
C D | Nuclease SbcCD subunit C | A0A037YDI0_ECOLX  
E | DNA (31-MER) |  
F | DNA (32-MER) |  
  
Non-standard residues in 6s85 #7  
---  
ADP — adenosine-5'-diphosphate  
MG — magnesium ion  
MN — manganese (II) ion  
  

> view #7

> hide #7 target a

> show #7 target c

> seme #7/ADP

Unknown command: seme #7/ADP  

> seme #7:ADP

Unknown command: seme #7:ADP  

> seme #7@ADP

Unknown command: seme #7@ADP  

> select #7/ADP

Nothing selected  

> select #7:ADP

54 atoms, 58 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel ball

Changed 54 atom styles  

> color sel byhetero

> select #7:MG

2 atoms, 2 residues, 1 model selected  

> style sel sphere

Changed 2 atom styles  

> show sel atoms

> style sel sphere

Changed 2 atom styles  

> select zone #7:MG 3.5 #7C/D residue true

Expected an objects specifier or a keyword  

> select zone #7:MG 3.5 #7/C/D residues true

Selected 95 atoms  

> select zone #7/C/D 3.5 #7:MG 3.5 residue true

Expected a keyword  

> select zone #7/C/D 3.5 #7:MG residues true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 63, in select_zone  
sa, ss = zone_items(na, ns, range, fa, fs, extend, residues)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
TypeError: NumPy array is not contiguous  
  
TypeError: NumPy array is not contiguous  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
  
See log for complete Python traceback.  
  

> select zone #7/C/D 3.5 #7:MG residues true

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 63, in select_zone  
sa, ss = zone_items(na, ns, range, fa, fs, extend, residues)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
TypeError: NumPy array is not contiguous  
  
TypeError: NumPy array is not contiguous  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
  
See log for complete Python traceback.  
  

> select zone #7/C/D 3.5 #7:MG

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 63, in select_zone  
sa, ss = zone_items(na, ns, range, fa, fs, extend, residues)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
TypeError: NumPy array is not contiguous  
  
TypeError: NumPy array is not contiguous  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
  
See log for complete Python traceback.  
  

> select zone #7/C 3.5 #7:MG

Nothing selected  

> select #7:MG

2 atoms, 2 residues, 1 model selected  

> color sel orange

> select zone #7 3.5 #7@MG

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 63, in select_zone  
sa, ss = zone_items(na, ns, range, fa, fs, extend, residues)  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
TypeError: NumPy array is not contiguous  
  
TypeError: NumPy array is not contiguous  
  
File
"/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/zonesel.py", line 97, in zone_items  
i1, i2 = find_close_points_sets(nxyz, fxyz, range)  
  
See log for complete Python traceback.  
  

> select zone #7@MG 3.5 #7

Selected 15 atoms  

> select zone #7@MG 3.5 #7 residues true

Selected 95 atoms  

> show sel atoms

> style sel ball

Changed 95 atom styles  

> color sel byhetero

> select zone #7@MG 3.7 #7 residues true

Selected 103 atoms  

> show sel atoms

> style sel ball

Changed 103 atom styles  

> color sel byhetero

> hide #!7 models

> view #6 clip false

> select #6/A/B

7045 atoms, 7031 bonds, 14 pseudobonds, 974 residues, 3 models selected  

> show sel surfaces

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 5dac_A SES surface #6.4: minimum, -15.13, mean -0.44,
maximum 13.55  
Coulombic values for 5dac_B SES surface #6.5: minimum, -14.56, mean -0.35,
maximum 14.23  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select clear

> save
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/ALPHAFOLD_IDRIS/AF_scRad50_rif2bat/5dac_mre11_hinge_dna_interaction.png
> width 1235 height 716 supersample 3

> hide #!6 surfaces

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/SMC_condensin/DNA_SMC2_SMC4/CHARMM/DNA_haddock_cluster_1.pdb

Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/SMC_condensin/DNA_SMC2_SMC4/CHARMM/DNA_haddock_cluster_1.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 ARG A 3
ASN A 34 1 32  
Start residue of secondary structure not found: HELIX 2 2 TYR A 43 PHE A 46 1
4  
Start residue of secondary structure not found: HELIX 3 3 VAL A 55 GLN A 57 1
3  
Start residue of secondary structure not found: HELIX 4 4 ASN A 63 TYR A 68 1
6  
Start residue of secondary structure not found: HELIX 5 5 ALA A 69 ALA A 76 1
8  
33 messages similar to the above omitted  
  
Chain information for DNA_haddock_cluster_1.pdb #8  
---  
Chain | Description  
B | No description available  
  

> mmaker #8 to #7

No chains in match structure DNA_haddock_cluster_1.pdb #8 compatible with
BLOSUM-62 similarity matrix  

> hide #!6 models

> view #8 clip false

> close #8

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/SMC_condensin/DNA_SMC2_SMC4/CHARMM/smc2smc4_dna_ch36.pdb
> segisChain true

'segisChain' has no suffix  

> open
> /Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/SMC_condensin/DNA_SMC2_SMC4/CHARMM/smc2smc4_dna_ch36.pdb
> segidChains true

Summary of feedback from opening
/Users/pc126390/Integrative_Modelling/Projet_Stephane_Marcand/SMC_condensin/DNA_SMC2_SMC4/CHARMM/smc2smc4_dna_ch36.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK SMC2SMC4 DNA  
  
Ignored bad PDB record found on line 2  
REMARK DATE: 3/10/23 10:58: 3 CREATED BY USER: pc126390  
  
Chain information for smc2smc4_dna_ch36.pdb #8  
---  
Chain | Description  
DNAE | No description available  
DNAF | No description available  
SMC2 | No description available  
SMC4 | No description available  
  

> mmaker #8 to #7

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 6s85, chain A (#7) with smc2smc4_dna_ch36.pdb, chain SMC2 (#8),
sequence alignment score = 68.8  
RMSD between 5 pruned atom pairs is 0.929 angstroms; (across all 155 pairs:
25.911)  
  

> view #8 clip false

> show #!7 models

> mmaker #8 to #6

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 5dac, chain A (#6) with smc2smc4_dna_ch36.pdb, chain SMC2 (#8),
sequence alignment score = 60.8  
RMSD between 4 pruned atom pairs is 1.146 angstroms; (across all 166 pairs:
30.106)  
  

> view #7 clip false

> hide #8 models

> show #8 models

> hide #8 models

> hide #!7 models

> show #!7 models

> show #8 models

> hide #!7 models

> mmaker #8 to #6

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 5dac, chain A (#6) with smc2smc4_dna_ch36.pdb, chain SMC2 (#8),
sequence alignment score = 60.8  
RMSD between 4 pruned atom pairs is 1.146 angstroms; (across all 166 pairs:
30.106)  
  

> show #!6 models

> view #7 clip false

> hide #!6 models

> view #8 clip false

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #8 models

> mmaker #8 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker scRap1_mre11_cutting_state, chain RADD (#2) with
smc2smc4_dna_ch36.pdb, chain SMC4 (#8), sequence alignment score = 64.2  
RMSD between 35 pruned atom pairs is 1.000 angstroms; (across all 153 pairs:
24.855)  
  

> show #2 models

> show #3 models

> hide #3 models

> show #8 models

> hide #!6 models

> show #!6 models

> hide #2 models

> hide #8 models

> show #1 models

> show #!4 models

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> mmaker #6 to #7

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 6s85, chain D (#7) with 5dac, chain A (#6), sequence alignment
score = 175.9  
RMSD between 66 pruned atom pairs is 1.248 angstroms; (across all 190 pairs:
6.325)  
  

> show #!7 models

> hide #!7 models

> show #!7 models

> show #5 models

> hide #5 models

> show #5 models

> hide #5 models

> show #5 models

> hide #1 models

> show #1 models

> hide #!6 models

> show #!6 models

> mmaker #6 to #1

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 1_AF2_scRad50_Bat_ranked_0, chain A (#1) with 5dac, chain A (#6),
sequence alignment score = 1282.2  
RMSD between 251 pruned atom pairs is 0.927 angstroms; (across all 376 pairs:
3.619)  
  

> hide #5 models

> show #5 models

> hide #5 models

> hide #1 models

> hide #!6 models

> show #!6 models

> hide #!7 models




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.9.11
Locale: fr_FR.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
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      Model Identifier: MacBookPro18,2
      Model Number: Z14X000ABFN/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 8419.41.10

Software:

    System Software Overview:

      System Version: macOS 13.0 (22A380)
      Kernel Version: Darwin 22.1.0
      Time since boot: 2 jours et 26 minutes

Graphics/Displays:

    Apple M1 Max:

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      Type: GPU
      Bus: Built-In
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      Vendor: Apple (0x106b)
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