The following bug report has been submitted:
Platform: macOS-11.2.3-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/ZF_comparison.cxs"
Log from Thu May 16 16:03:08 2024 Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/fxy/OneDrive - connect.hku.hk/From Herbert/SH/hMCM-
> SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2 interaction).pdb" format pdb
Chain information for hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb #1
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
> select add #1
29221 atoms, 29669 bonds, 6 pseudobonds, 3736 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> select ::name="ATP"
62 atoms, 66 bonds, 2 residues, 1 model selected
> select ::name="ADP"::name="ATP"::name="MG"::name="ZN"
148 atoms, 153 bonds, 2 pseudobonds, 10 residues, 2 models selected
> show sel surfaces
> hide sel cartoons
> close session
> open 7w1y format mmcif fromDatabase pdb
Summary of feedback from opening 7w1y fetched from pdb
---
warnings | Ignoring microheterogeneity for label_seq_id 1 in chain
Ignoring microheterogeneity for label_seq_id 2 in chain S
Ignoring microheterogeneity for label_seq_id 3 in chain S
Ignoring microheterogeneity for label_seq_id 4 in chain S
Ignoring microheterogeneity for label_seq_id 5 in chain S
93 messages similar to the above omitted
7w1y title:
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) [more
info...]
Chain information for 7w1y #1
---
Chain | Description | UniProt
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904
3 B | Isoform 2 of DNA replication licensing factor MCM3 | MCM3_HUMAN -44-808
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719
O | DNA (49-MER) |
S | DNA (49-MER) |
Non-standard residues in 7w1y #1
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> select
66630 atoms, 67929 bonds, 192 pseudobonds, 8266 residues, 4 models selected
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> hide sel surfaces
> select ::name="ADP"::name="ATP"::name="MG"::name="ZN"
378 atoms, 380 bonds, 20 pseudobonds, 34 residues, 2 models selected
> show sel cartoons
> show sel surfaces
> close session
> open 6XTY format mmcif fromDatabase pdb
6xty title:
CryoEM structure of human CMG bound to AND-1 (CMGA) [more info...]
Chain information for 6xty #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904
3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 1-853
4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863
5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734
6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821
7 | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719
A | DNA replication complex GINS protein PSF1 | PSF1_HUMAN 1-196
B | DNA replication complex GINS protein PSF2 | PSF2_HUMAN 1-185
C | DNA replication complex GINS protein PSF3 | PSF3_HUMAN 1-216
D | DNA replication complex GINS protein SLD5 | SLD5_HUMAN 1-223
E | Cell division control protein 45 homolog | CDC45_HUMAN 1-566
F G H | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN 1-1129
Non-standard residues in 6xty #1
---
ZN — zinc ion
> select
48749 atoms, 49670 bonds, 39 pseudobonds, 6122 residues, 3 models selected
> hide sel atoms
> hide sel surfaces
> show sel cartoons
> select ::name="ZN"
5 atoms, 5 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> close session
> open 3JA8 format mmcif fromDatabase pdb
3ja8 title:
Cryo-EM structure of the MCM2-7 double hexamer [more info...]
Chain information for 3ja8 #1
---
Chain | Description | UniProt
2 | Minichromosome Maintenance 2 | MCM2_YEAST 1-868
3 | Minichromosome Maintenance 3 | MCM3_YEAST 1-971
4 | Minichromosome Maintenance 4 | MCM4_YEAST 1-933
5 | Minichromosome Maintenance 5 | MCM5_YEAST 1-775
6 | Minichromosome Maintenance 6 | MCM6_YEAST 1-1017
7 | Minichromosome Maintenance 7 | MCM7_YEAST 1-845
Non-standard residues in 3ja8 #1
---
ADP — adenosine-5'-diphosphate
> select
29838 atoms, 30307 bonds, 20 pseudobonds, 3792 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select ::name="ADP"
162 atoms, 174 bonds, 6 residues, 1 model selected
> show sel surfaces
> close session
> open 3ja8 format mmcif fromDatabase pdb
3ja8 title:
Cryo-EM structure of the MCM2-7 double hexamer [more info...]
Chain information for 3ja8 #1
---
Chain | Description | UniProt
2 | Minichromosome Maintenance 2 | MCM2_YEAST 1-868
3 | Minichromosome Maintenance 3 | MCM3_YEAST 1-971
4 | Minichromosome Maintenance 4 | MCM4_YEAST 1-933
5 | Minichromosome Maintenance 5 | MCM5_YEAST 1-775
6 | Minichromosome Maintenance 6 | MCM6_YEAST 1-1017
7 | Minichromosome Maintenance 7 | MCM7_YEAST 1-845
Non-standard residues in 3ja8 #1
---
ADP — adenosine-5'-diphosphate
> select
29838 atoms, 30307 bonds, 20 pseudobonds, 3792 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> select ::name="ADP"
162 atoms, 174 bonds, 6 residues, 1 model selected
> show sel surfaces
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '^' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a7' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\ufb02' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a7' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\ufb02' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '6' for virtual key 22 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 6wgg
6wgg title:
Atomic model of pre-insertion mutant OCCM-DNA complex(ORC-Cdc6-Cdt1-Mcm2-7
with Mcm6 WHD truncation) [more info...]
Chain information for 6wgg #2
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-961
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
8 | Cell division cycle protein CDT1 | CDT1_YEAST 1-604
9 | Cell division control protein 6 | CDC6_YEAST 1-513
A | Origin recognition complex subunit 1 | ORC1_YEAST 1-913
B | Origin recognition complex subunit 2 | ORC2_YEAST 1-620
C | Origin recognition complex subunit 3 | ORC3_YEAST 1-616
D | Origin recognition complex subunit 4 | ORC4_YEAST 1-529
E | Origin recognition complex subunit 5 | ORC5_YEAST 1-479
F | Origin recognition complex subunit 6 | ORC6_YEAST 1-435
G | DNA (41-MER) |
H | DNA (41-MER) |
Non-standard residues in 6wgg #2
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
> close #1
> select add #2
54601 atoms, 55672 bonds, 155 pseudobonds, 6860 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> select ::name="AGS"
124 atoms, 132 bonds, 4 residues, 1 model selected
> show sel surfaces
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1d' for virtual key 124 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select ~sel & ##selected
54477 atoms, 55540 bonds, 155 pseudobonds, 6856 residues, 3 models selected
> open 5h7i
Summary of feedback from opening 5h7i fetched from pdb
---
warning | PDB entry 5H7I has been replaced by 5XF8
5h7i title:
Cryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state [more info...]
Chain information for 5h7i #1
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1018
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
C | Cell division cycle protein CDT1 | CDT1_YEAST 1-604
> hide #!2 models
> select add #2
54601 atoms, 55672 bonds, 155 pseudobonds, 6860 residues, 3 models selected
> select subtract #2
4 models selected
> select add #1
21016 atoms, 20977 bonds, 36 pseudobonds, 4243 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> select ::name="AGS"
124 atoms, 132 bonds, 4 residues, 1 model selected
> show #!1 surfaces
> hide #!1 surfaces
> close #2
> ui tool show "Show Sequence Viewer"
> open 5h7i
Summary of feedback from opening 5h7i fetched from pdb
---
warning | PDB entry 5H7I has been replaced by 5XF8
5h7i title:
Cryo-EM structure of the Cdt1-MCM2-7 complex in AMPPNP state [more info...]
Chain information for 5h7i #2
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1018
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
C | Cell division cycle protein CDT1 | CDT1_YEAST 1-604
> close #2
> ui tool show "Show Sequence Viewer"
> sequence chain /3
Alignment identifier is 1/3
> open "/Users/fxy/OneDrive - connect.hku.hk/From Herbert/SH/hMCM-
> SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2 interaction).pdb"
Chain information for hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb #2
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
> select add #2
29221 atoms, 29669 bonds, 6 pseudobonds, 3736 residues, 2 models selected
> show sel cartoons
> hide sel atoms
Drag select of 295 residues
> select #2/2:243
7 atoms, 6 bonds, 1 residue, 1 model selected
> select add #2
29221 atoms, 29669 bonds, 6 pseudobonds, 3736 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
29221 atoms, 29669 bonds, 6 pseudobonds, 3736 residues, 2 models selected
Drag select of 70 residues
> select add #2
29221 atoms, 29669 bonds, 6 pseudobonds, 3736 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,27.231,0,1,0,-2.972,0,0,1,-16.578
> view matrix models #2,1,0,0,-36.855,0,1,0,7.4085,0,0,1,56.21
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.29388,0.37567,0.87893,-161.41,-0.94653,-0.013689,0.32233,355.23,0.13312,-0.92665,0.35156,370.06
> view matrix models
> #2,-0.22641,0.25051,0.94127,-39.488,-0.90267,-0.41704,-0.10614,526.3,0.36596,-0.87368,0.32055,316.83
> view matrix models
> #2,-0.052208,0.29068,0.9554,-87.479,-0.99687,-0.071971,-0.032577,454.91,0.059292,-0.95411,0.29353,403.89
> view matrix models
> #2,-0.00069759,0.33656,0.94166,-105.21,-0.93772,-0.32735,0.1163,466.09,0.3474,-0.88293,0.31583,323.72
> view matrix models
> #2,-0.057672,0.52974,0.8462,-114.83,-0.93462,-0.3266,0.14076,460.01,0.35093,-0.78276,0.51394,258.46
> select subtract #2
Nothing selected
> ui tool show Matchmaker
> matchmaker #1/2 to #2/2 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 2 (#2) with 5h7i, chain 2 (#1), sequence alignment
score = 1784.9
RMSD between 240 pruned atom pairs is 1.305 angstroms; (across all 572 pairs:
3.879)
> matchmaker #1/3 to #2/3 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 3 (#2) with 5h7i, chain 3 (#1), sequence alignment
score = 1329
RMSD between 273 pruned atom pairs is 1.303 angstroms; (across all 489 pairs:
6.580)
> matchmaker #1/2 to #2/2 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 2 (#2) with 5h7i, chain 2 (#1), sequence alignment
score = 1784.9
RMSD between 240 pruned atom pairs is 1.305 angstroms; (across all 572 pairs:
3.879)
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> select add #1
21016 atoms, 20977 bonds, 36 pseudobonds, 4243 residues, 2 models selected
> color (#!1 & sel) dark gray
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #2/2
5375 atoms, 5474 bonds, 1 pseudobond, 679 residues, 2 models selected
> color (#!2 & sel) orange
> select #2/3
4724 atoms, 4784 bonds, 609 residues, 1 model selected
> color sel cyan
> select #2/4
5202 atoms, 5286 bonds, 682 residues, 1 model selected
> color sel magenta
> select #2/
Expected an objects specifier or a keyword
> select #2/5
4411 atoms, 4468 bonds, 564 residues, 1 model selected
> color sel yellow
> select #2/6
5334 atoms, 5420 bonds, 1 pseudobond, 670 residues, 2 models selected
> color (#!2 & sel) medium blue
> select #2/7
4173 atoms, 4237 bonds, 530 residues, 1 model selected
> color sel forest green
> select add #2
29221 atoms, 29669 bonds, 6 pseudobonds, 3736 residues, 2 models selected
> select subtract #2
Nothing selected
> hide #!1 models
> show #!1 models
> set bgColor white
> set bgColor gray
> set bgColor black
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'O' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 6rqc
Summary of feedback from opening 6rqc fetched from pdb
---
warning | Atom HO5' is not in the residue template for DT /X:1
6rqc title:
Cryo-EM structure of an MCM loading intermediate [more info...]
Chain information for 6rqc #3
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
A | Origin recognition complex subunit 1 | ORC1_YEAST 1-914
B | Origin recognition complex subunit 2 | ORC2_YEAST 1-620
C | Origin recognition complex subunit 3 | ORC3_YEAST 1-616
D | Origin recognition complex subunit 4 | ORC4_YEAST 1-529
E | Origin recognition complex subunit 5 | ORC5_YEAST 1-479
F | Origin recognition complex subunit 6 | ORC6_YEAST 1-435
X | DNA (88-MER) |
Y | DNA (88-MER) |
Non-standard residues in 6rqc #3
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> hide #!1 models
> hide #!2 models
> select add #3
105307 atoms, 106613 bonds, 262 pseudobonds, 6365 residues, 4 models selected
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #3/2 to #2/2 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 2 (#2) with 6rqc, chain 2 (#3), sequence alignment
score = 1686.5
RMSD between 90 pruned atom pairs is 1.263 angstroms; (across all 582 pairs:
18.916)
> show #!2 models
> hide #!2 models
> close #3
> open 5udb
Summary of feedback from opening 5udb fetched from pdb
---
warning | PDB entry 5UDB has been replaced by 5V8F
5udb title:
Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1
[more info...]
Chain information for 5udb #3
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
8 | Cell division cycle protein CDT1 | CDT1_YEAST 1-604
9 | Cell division control protein 6 | CDC6_YEAST 1-513
A | Origin recognition complex subunit 1 | ORC1_YEAST 1-914
B | Origin recognition complex subunit 2 | ORC2_YEAST 1-620
C | Origin recognition complex subunit 3 | ORC3_YEAST 1-616
D | Origin recognition complex subunit 4 | ORC4_YEAST 1-529
E | Origin recognition complex subunit 5 | ORC5_YEAST 1-479
F | Origin recognition complex subunit 6 | ORC6_YEAST 1-435
M | DNA (39-MER) |
N | DNA (39-MER) |
Non-standard residues in 5udb #3
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
> select add #3
57577 atoms, 58718 bonds, 124 pseudobonds, 7075 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> hide sel surfaces
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #3/2 to #2/2 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 2 (#2) with 5udb, chain 2 (#3), sequence alignment
score = 1665.2
RMSD between 249 pruned atom pairs is 1.233 angstroms; (across all 569 pairs:
4.325)
> show #!1 models
> show #!2 models
> select subtract #3
Nothing selected
> color #3 #d4c7c9ff
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> select #3/8
4163 atoms, 4240 bonds, 4 pseudobonds, 519 residues, 2 models selected
> color (#!3 & sel) lime
> show #!1 models
> select #1/7
3076 atoms, 3071 bonds, 4 pseudobonds, 622 residues, 2 models selected
> color (#!1 & sel) light sea green
> ui tool show "Color Actions"
> color sel hot pink
[Repeated 3 time(s)]
> undo
> color (#!1 & sel) dark gray
> select #1/8
Nothing selected
> ui tool show "Show Sequence Viewer"
> select #1/C
2131 atoms, 2126 bonds, 4 pseudobonds, 429 residues, 2 models selected
> color (#!1 & sel) hot pink
> select add #1
21016 atoms, 20977 bonds, 36 pseudobonds, 4243 residues, 3 models selected
> select subtract #1
7 models selected
> open 6WGC
6wgc title:
Atomic model of semi-attached mutant OCCM-DNA complex (ORC-Cdc6-Cdt1-Mcm2-7
with Mcm6 WHD truncation) [more info...]
Chain information for 6wgc #4
---
Chain | Description | UniProt
3 | DNA replication licensing factor MCM3 | MCM3_YEAST -9-961
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
9 | Cell division control protein 6 | CDC6_YEAST 1-513
A | Origin recognition complex subunit 1 | ORC1_YEAST 1-913
B | Origin recognition complex subunit 2 | ORC2_YEAST 1-620
C | Origin recognition complex subunit 3 | ORC3_YEAST 1-616
D | Origin recognition complex subunit 4 | ORC4_YEAST 1-529
E | Origin recognition complex subunit 5 | ORC5_YEAST 1-479
F | Origin recognition complex subunit 6 | ORC6_YEAST 1-435
G | DNA (41-MER) |
H | DNA (41-MER) |
Non-standard residues in 6wgc #4
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
> open 6WGG
6wgg title:
Atomic model of pre-insertion mutant OCCM-DNA complex(ORC-Cdc6-Cdt1-Mcm2-7
with Mcm6 WHD truncation) [more info...]
Chain information for 6wgg #5
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-961
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
8 | Cell division cycle protein CDT1 | CDT1_YEAST 1-604
9 | Cell division control protein 6 | CDC6_YEAST 1-513
A | Origin recognition complex subunit 1 | ORC1_YEAST 1-913
B | Origin recognition complex subunit 2 | ORC2_YEAST 1-620
C | Origin recognition complex subunit 3 | ORC3_YEAST 1-616
D | Origin recognition complex subunit 4 | ORC4_YEAST 1-529
E | Origin recognition complex subunit 5 | ORC5_YEAST 1-479
F | Origin recognition complex subunit 6 | ORC6_YEAST 1-435
G | DNA (41-MER) |
H | DNA (41-MER) |
Non-standard residues in 6wgg #5
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
> open 6WGI
Summary of feedback from opening 6WGI fetched from pdb
---
note | Fetching compressed mmCIF 6wgi from
http://files.rcsb.org/download/6wgi.cif
6wgi title:
Atomic model of the mutant OCCM (ORC-Cdc6-Cdt1-Mcm2-7 with Mcm6 WHD
truncation) loaded on DNA at 10.5 A resolution [more info...]
Chain information for 6wgi #6
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-961
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
9 | Cell division control protein 6 | CDC6_YEAST 1-513
A | Origin recognition complex subunit 1 | ORC1_YEAST 1-913
B | Origin recognition complex subunit 2 | ORC2_YEAST 1-620
C | Origin recognition complex subunit 3 | ORC3_YEAST 1-616
D | Origin recognition complex subunit 4 | ORC4_YEAST 1-529
E | Origin recognition complex subunit 5 | ORC5_YEAST 1-479
F | Origin recognition complex subunit 6 | ORC6_YEAST 1-435
G | DNA (34-MER) |
H | DNA (34-MER) |
L | Cell division cycle protein CDT1 | CDT1_YEAST 1-604
Non-standard residues in 6wgi #6
---
AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine
5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate);
adenosine-5'-diphosphate monothiophosphate)
MG — magnesium ion
> open 6WGF
6wgf title:
Atomic model of mutant Mcm2-7 hexamer with Mcm6 WHD truncation [more info...]
Chain information for 6wgf #7
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> select add #7
26076 atoms, 26437 bonds, 42 pseudobonds, 3435 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> hide sel atoms
[Repeated 1 time(s)]
> ui tool show Matchmaker
> matchmaker #7/2 to #2/2 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 2 (#2) with 6wgf, chain 2 (#7), sequence alignment
score = 1628.8
RMSD between 171 pruned atom pairs is 1.135 angstroms; (across all 493 pairs:
4.411)
> matchmaker #6/2 to #2/2 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 2 (#2) with 6wgi, chain 2 (#6), sequence alignment
score = 1713.4
RMSD between 242 pruned atom pairs is 1.269 angstroms; (across all 555 pairs:
4.337)
> matchmaker #5/2 to #2/2 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 2 (#2) with 6wgg, chain 2 (#5), sequence alignment
score = 1741.6
RMSD between 225 pruned atom pairs is 1.334 angstroms; (across all 562 pairs:
4.151)
> show #!4 models
> select subtract #7
Nothing selected
> select add #4
24605 atoms, 25232 bonds, 114 pseudobonds, 2890 residues, 3 models selected
> hide sel surfaces
> hide sel atoms
> show sel cartoons
> select subtract #4
Nothing selected
> ui tool show "Show Sequence Viewer"
> show #!5 models
> hide #!4 models
> select add #4
24605 atoms, 25232 bonds, 114 pseudobonds, 2890 residues, 3 models selected
> select subtract #4
Nothing selected
> select add #5
54601 atoms, 55672 bonds, 155 pseudobonds, 6860 residues, 3 models selected
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> select subtract #5
Nothing selected
> show #!6 models
> select add #6
52948 atoms, 53963 bonds, 150 pseudobonds, 6695 residues, 4 models selected
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> select subtract #6
Nothing selected
> hide #!5 models
> hide #!6 models
> hide #!1 models
> show #!1 models
> color #7 #e8bd83ff
> show #!2 models
> hide #!1 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/5
Alignment identifier is 2/5
> select #2/5:253-254
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #2/5:253-291
178 atoms, 178 bonds, 23 residues, 1 model selected
> show #!7 models
> color #7 #d8cd96ff
> color #7 #d8cddfff
> show #!6 models
> hide #!7 models
> show #!5 models
> hide #!6 models
> color #5 #c7bdcdff
> show #!6 models
> hide #!5 models
> hide #!2 models
> hide #!6 models
> show #!5 models
> select #4/D
3582 atoms, 3645 bonds, 3 pseudobonds, 437 residues, 2 models selected
> select #5/D
3582 atoms, 3645 bonds, 3 pseudobonds, 437 residues, 2 models selected
> show #!4 models
> hide #!4 models
> show #!3 models
> hide #!5 models
> select #3/D
3646 atoms, 3712 bonds, 2 pseudobonds, 448 residues, 2 models selected
> color (#!3 & sel) lime
> ui tool show "Color Actions"
> color sel salmon
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!4 models
> open 6qrc
6qrc title:
Crystal structure of TrmD, a tRNA-(N1G37) methyltransferase, from
Mycobacterium abscessus in complex with inhibitor [more info...]
Chain information for 6qrc #8
---
Chain | Description | UniProt
A B | tRNA (guanine-N(1)-)-methyltransferase | B1MDI3_MYCA9 1-242
Non-standard residues in 6qrc #8
---
JFE — 3-[1-[(3-methoxyphenyl)methyl]indol-6-yl]-1~{H}-pyrazol-5-amine
SO4 — sulfate ion
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!8 models
> hide #!8 models
> close #8
> open 6rqc
Summary of feedback from opening 6rqc fetched from pdb
---
warning | Atom HO5' is not in the residue template for DT /X:1
6rqc title:
Cryo-EM structure of an MCM loading intermediate [more info...]
Chain information for 6rqc #8
---
Chain | Description | UniProt
2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868
3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-971
4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933
5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775
6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017
7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-845
A | Origin recognition complex subunit 1 | ORC1_YEAST 1-914
B | Origin recognition complex subunit 2 | ORC2_YEAST 1-620
C | Origin recognition complex subunit 3 | ORC3_YEAST 1-616
D | Origin recognition complex subunit 4 | ORC4_YEAST 1-529
E | Origin recognition complex subunit 5 | ORC5_YEAST 1-479
F | Origin recognition complex subunit 6 | ORC6_YEAST 1-435
X | DNA (88-MER) |
Y | DNA (88-MER) |
Non-standard residues in 6rqc #8
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> select add #3
57577 atoms, 58718 bonds, 124 pseudobonds, 7075 residues, 3 models selected
> select subtract #3
Nothing selected
> select add #8
105307 atoms, 106613 bonds, 262 pseudobonds, 6365 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> select ::name="ADP"::name="AGS"::name="ATP"::name="MG"::name="ZN"
1063 atoms, 1112 bonds, 15 pseudobonds, 47 residues, 9 models selected
> show sel & #!8 surfaces
> hide #!8 models
> select add #8
106077 atoms, 107426 bonds, 268 pseudobonds, 6397 residues, 20 models selected
> select subtract #8
770 atoms, 813 bonds, 6 pseudobonds, 32 residues, 16 models selected
> select add #6
53592 atoms, 54644 bonds, 152 pseudobonds, 6721 residues, 9 models selected
> select subtract #6
644 atoms, 681 bonds, 2 pseudobonds, 26 residues, 5 models selected
> select add #5
55121 atoms, 56221 bonds, 157 pseudobonds, 6882 residues, 7 models selected
> select subtract #5
520 atoms, 549 bonds, 2 pseudobonds, 22 residues, 4 models selected
> select add #4
25001 atoms, 25649 bonds, 116 pseudobonds, 2908 residues, 6 models selected
> select subtract #4
396 atoms, 417 bonds, 2 pseudobonds, 18 residues, 3 models selected
> select add #3
57725 atoms, 58871 bonds, 126 pseudobonds, 7085 residues, 5 models selected
> select subtract #3
148 atoms, 153 bonds, 2 pseudobonds, 10 residues, 2 models selected
> select add #2
29221 atoms, 29669 bonds, 6 pseudobonds, 3736 residues, 2 models selected
> select subtract #2
Nothing selected
> show #!7 models
> select add #7
26076 atoms, 26437 bonds, 42 pseudobonds, 3435 residues, 2 models selected
> select ::name="ADP"::name="AGS"::name="ATP"::name="MG"::name="ZN"
1063 atoms, 1112 bonds, 15 pseudobonds, 47 residues, 9 models selected
> show #!7 surfaces
> hide #!7 surfaces
> select add #6
53885 atoms, 54943 bonds, 161 pseudobonds, 6736 residues, 20 models selected
> select subtract #6
937 atoms, 980 bonds, 11 pseudobonds, 41 residues, 16 models selected
> select add #5
55414 atoms, 56520 bonds, 166 pseudobonds, 6897 residues, 18 models selected
> select subtract #5
813 atoms, 848 bonds, 11 pseudobonds, 37 residues, 15 models selected
> select add #4
25294 atoms, 25948 bonds, 125 pseudobonds, 2923 residues, 17 models selected
> select subtract #4
689 atoms, 716 bonds, 11 pseudobonds, 33 residues, 14 models selected
> select add #3
58018 atoms, 59170 bonds, 135 pseudobonds, 7100 residues, 16 models selected
> select subtract #3
441 atoms, 452 bonds, 11 pseudobonds, 25 residues, 13 models selected
> select add #2
29514 atoms, 29968 bonds, 15 pseudobonds, 3751 residues, 13 models selected
> select subtract #2
293 atoms, 299 bonds, 9 pseudobonds, 15 residues, 11 models selected
> select add #8
105307 atoms, 106613 bonds, 262 pseudobonds, 6365 residues, 13 models selected
> select subtract #8
9 models selected
> select add #7
26076 atoms, 26437 bonds, 42 pseudobonds, 3435 residues, 2 models selected
> select ::name="ADP"::name="AGS"::name="ATP"::name="MG"::name="ZN"
1063 atoms, 1112 bonds, 15 pseudobonds, 47 residues, 9 models selected
> show #!7 surfaces
> select add #7
27139 atoms, 27549 bonds, 57 pseudobonds, 3482 residues, 20 models selected
> select subtract #7
1063 atoms, 1112 bonds, 15 pseudobonds, 47 residues, 24 models selected
> select add #7
27139 atoms, 27549 bonds, 57 pseudobonds, 3482 residues, 20 models selected
> hide sel & #!7 surfaces
> select subtract #7
1063 atoms, 1112 bonds, 15 pseudobonds, 47 residues, 24 models selected
> select add #2
30136 atoms, 30628 bonds, 19 pseudobonds, 3773 residues, 18 models selected
> select subtract #2
915 atoms, 959 bonds, 13 pseudobonds, 37 residues, 16 models selected
> select add #3
58244 atoms, 59413 bonds, 137 pseudobonds, 7104 residues, 18 models selected
> select subtract #3
667 atoms, 695 bonds, 13 pseudobonds, 29 residues, 15 models selected
> select add #4
25148 atoms, 25795 bonds, 127 pseudobonds, 2915 residues, 17 models selected
> select subtract #4
543 atoms, 563 bonds, 13 pseudobonds, 25 residues, 14 models selected
> select add #5
55020 atoms, 56103 bonds, 168 pseudobonds, 6881 residues, 16 models selected
> select subtract #5
419 atoms, 431 bonds, 13 pseudobonds, 21 residues, 13 models selected
> select add #6
53241 atoms, 54262 bonds, 159 pseudobonds, 6710 residues, 15 models selected
> select subtract #6
293 atoms, 299 bonds, 9 pseudobonds, 15 residues, 11 models selected
> select add #8
105307 atoms, 106613 bonds, 262 pseudobonds, 6365 residues, 13 models selected
> select subtract #8
9 models selected
> select add #7
26076 atoms, 26437 bonds, 42 pseudobonds, 3435 residues, 2 models selected
> select ::name="ATP"
191 atoms, 201 bonds, 5 residues, 2 models selected
> select ::name="ATP"
191 atoms, 201 bonds, 5 residues, 2 models selected
> select ::name="ADP"
237 atoms, 251 bonds, 7 residues, 2 models selected
> hide #!7 models
> show #!8 models
> select ::name="ADP"
237 atoms, 251 bonds, 7 residues, 2 models selected
> select ::name="ATP"
191 atoms, 201 bonds, 5 residues, 2 models selected
> select ::name="AGS"
620 atoms, 660 bonds, 20 residues, 4 models selected
> hide #!8 models
> show #!3 models
> show sel & #!3 surfaces
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show sel & #!5 surfaces
> show #!6 models
> hide #!5 models
> show sel & #!6 surfaces
> hide #!6 models
> select add #3
57949 atoms, 59114 bonds, 124 pseudobonds, 7087 residues, 22 models selected
> select subtract #3
372 atoms, 396 bonds, 12 residues, 19 models selected
> select add #4
24853 atoms, 25496 bonds, 114 pseudobonds, 2898 residues, 13 models selected
> select subtract #4
248 atoms, 264 bonds, 8 residues, 10 models selected
> select add #5
54725 atoms, 55804 bonds, 155 pseudobonds, 6864 residues, 12 models selected
> select subtract #5
124 atoms, 132 bonds, 4 residues, 9 models selected
> select add #6
52948 atoms, 53963 bonds, 150 pseudobonds, 6695 residues, 8 models selected
> select subtract #6
4 models selected
> show #!2 models
> show #!7 models
> hide #!2 models
> show #!2 models
Mismatch between Cocoa '\x0' and Carbon 'e' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'E' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'e' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'e' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b4' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b4' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b4' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00b4' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x5' for virtual key 14 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon 'l' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'L' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'l' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'l' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ac' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d2' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ac' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d2' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #2/5:160-220
63 atoms, 61 bonds, 9 residues, 1 model selected
> hide #!7 models
> show #!7 models
> hide #!7 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/3
Alignment identifier is 2/3
> select #2/3:138-184
52 atoms, 52 bonds, 6 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/7
Alignment identifier is 2/7
> select #2/7:173-227
244 atoms, 246 bonds, 31 residues, 1 model selected
> select
> #2/7:5-18,28-37,49-51,60-65,67-84,328-335,344-354,383-393,429-432,443-445,448-459,497-500,505-510,523-538,552-563,571-591,599-613,623-634
1506 atoms, 1509 bonds, 186 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #2/4
Alignment identifier is 2/4
> select #2/4:296-357
483 atoms, 491 bonds, 61 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon 'p' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'P' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'p' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'p' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03c0' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u220f' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u03c0' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u220f' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x10' for virtual key 35 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon 'n' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'N' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'n' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'n' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02dc' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02dc' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '~' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02dc' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xe' for virtual key 45 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 7W1Y
Summary of feedback from opening 7W1Y fetched from pdb
---
warnings | Ignoring microheterogeneity for label_seq_id 1 in chain
Ignoring microheterogeneity for label_seq_id 2 in chain S
Ignoring microheterogeneity for label_seq_id 3 in chain S
Ignoring microheterogeneity for label_seq_id 4 in chain S
Ignoring microheterogeneity for label_seq_id 5 in chain S
93 messages similar to the above omitted
7w1y title:
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) [more
info...]
Chain information for 7w1y #9
---
Chain | Description | UniProt
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904
3 B | Isoform 2 of DNA replication licensing factor MCM3 | MCM3_HUMAN -44-808
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719
O | DNA (49-MER) |
S | DNA (49-MER) |
Non-standard residues in 7w1y #9
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> select add #2
29221 atoms, 29669 bonds, 6 pseudobonds, 3736 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #9
66630 atoms, 67929 bonds, 192 pseudobonds, 8266 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> hide sel surfaces
> ui tool show Matchmaker
> matchmaker #9/2 to #2/2 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 2 (#2) with 7w1y, chain 2 (#9), sequence alignment
score = 3175.1
RMSD between 341 pruned atom pairs is 0.852 angstroms; (across all 677 pairs:
18.072)
> select subtract #9
Nothing selected
> color #9 #6ef4e4ff
> color #9 #adf3f4ff
> color #9 #d5f4c8ff
> select #9/2
5624 atoms, 5726 bonds, 9 pseudobonds, 709 residues, 3 models selected
> color (#!9 & sel) cornflower blue
> ui tool show Matchmaker
> matchmaker #9/6 to #2/6 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 6 (#2) with 7w1y, chain 6 (#9), sequence alignment
score = 3078.8
RMSD between 269 pruned atom pairs is 0.685 angstroms; (across all 668 pairs:
11.855)
> ui tool show Matchmaker
> matchmaker #9/3 to #2/3 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 3 (#2) with 7w1y, chain 3 (#9), sequence alignment
score = 2547
RMSD between 241 pruned atom pairs is 1.069 angstroms; (across all 538 pairs:
13.658)
> select #2/7:520-330
Nothing selected
> show #!2,9 surfaces
> hide #!2,9 surfaces
> select #2/7:320-330
85 atoms, 86 bonds, 10 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #9/5 to #2/5 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 5 (#2) with 7w1y, chain 5 (#9), sequence alignment
score = 2333.5
RMSD between 217 pruned atom pairs is 0.957 angstroms; (across all 559 pairs:
19.150)
> color #9 #a5f4bfff
> color #9 #c1f4c6ff
> color #9 #d0f4cdff
> color #9 #e7f4efff
> select #2/5
4411 atoms, 4468 bonds, 564 residues, 1 model selected
> color (#!2 & sel) light sea green
> select #9/5
5529 atoms, 5614 bonds, 10 pseudobonds, 713 residues, 3 models selected
> color (#!9 & sel) light sea green
> open "/Users/fxy/OneDrive - connect.hku.hk/From Herbert/Pre-
> DH/sDH_aligned_12.pdb"
Summary of feedback from opening /Users/fxy/OneDrive - connect.hku.hk/From
Herbert/Pre-DH/sDH_aligned_12.pdb
---
warnings | Start residue of secondary structure not found: HELIX 54 54 ALA 3
10 LEU 3 23 1 14
Start residue of secondary structure not found: HELIX 206 206 ALA B 10 LEU B
23 1 14
Chain information for sDH_aligned_12.pdb #10
---
Chain | Description
2 A | No description available
3 B | No description available
4 | No description available
5 D | No description available
6 | No description available
7 F | No description available
C | No description available
E | No description available
> select add #10
66475 atoms, 67505 bonds, 19 pseudobonds, 8540 residues, 7 models selected
> select add #9
127576 atoms, 129820 bonds, 201 pseudobonds, 16093 residues, 8 models selected
> select subtract #9
60946 atoms, 61891 bonds, 9 pseudobonds, 7827 residues, 17 models selected
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> ui tool show Matchmaker
> matchmaker #10/5 to #2/5 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 5 (#2) with sDH_aligned_12.pdb, chain 5 (#10),
sequence alignment score = 2480.6
RMSD between 508 pruned atom pairs is 0.950 angstroms; (across all 558 pairs:
2.098)
> select subtract #10
Nothing selected
> color #10 #b8f0a1ff
> color #10 #f0d6c5ff
> hide #!9 models
> hide #!2 models
> show #!9 models
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #9/3 to #10/3 pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
> select #9/3
5112 atoms, 5192 bonds, 4 pseudobonds, 652 residues, 3 models selected
> color (#!9 & sel) light sea green
> select #10/3
5075 atoms, 5142 bonds, 653 residues, 1 model selected
> color sel hot pink
> ui tool show Matchmaker
> matchmaker #9/3 & sel to #10/3 & sel pairing ss
No molecules/chains to match specified
> select #10/3:1-400
2860 atoms, 2896 bonds, 368 residues, 1 model selected
> select #10/3:1-300
2140 atoms, 2168 bonds, 268 residues, 1 model selected
> select #10/3:1-250
1810 atoms, 1836 bonds, 226 residues, 1 model selected
> select #10/3:1-220
1613 atoms, 1636 bonds, 200 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #9/3 to #10/3 & sel pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 919.3
RMSD between 150 pruned atom pairs is 0.684 angstroms; (across all 200 pairs:
3.166)
> select clear
> color #9 #bbf6eaff
> select #10/3:173-227
389 atoms, 394 bonds, 49 residues, 1 model selected
> color sel forest green
> select #10/7:173-227
367 atoms, 369 bonds, 55 residues, 1 model selected
> color sel forest green
> select #9/7:173-227
422 atoms, 430 bonds, 55 residues, 1 model selected
> hide #!10 models
> hide #!9 models
> show #!10 models
> select #10/7:173-227
367 atoms, 369 bonds, 55 residues, 1 model selected
> show #!9 models
> hide #!10 models
> hide #!9 models
> show #!10 models
> show #!9 models
> select #9/6:157-198
347 atoms, 351 bonds, 42 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #10/6 to #9/6 pairing ss
Parameters
---
Chain pairing | ss
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 7w1y, chain 6 (#9) with sDH_aligned_12.pdb, chain 6 (#10), sequence
alignment score = 3069.2
RMSD between 286 pruned atom pairs is 0.713 angstroms; (across all 668 pairs:
11.931)
> select #9/2
5624 atoms, 5726 bonds, 9 pseudobonds, 709 residues, 3 models selected
> color (#!9 & sel) orange
> select #9/6
5755 atoms, 5846 bonds, 8 pseudobonds, 719 residues, 3 models selected
> color (#!9 & sel) medium blue
> select #9/4
5220 atoms, 5311 bonds, 9 pseudobonds, 656 residues, 3 models selected
> color (#!9 & sel) magenta
> select #9/2,#9/4,#9/6
Expected an objects specifier or a keyword
> select #9/2, #9/4, #9/6
Expected an objects specifier or a keyword
> select #9/2, 4, 6
16599 atoms, 16883 bonds, 26 pseudobonds, 2084 residues, 3 models selected
> select ~sel & ##selected
50031 atoms, 51046 bonds, 166 pseudobonds, 6182 residues, 4 models selected
> hide sel cartoons
> select #10/2, 4, 6
15911 atoms, 16179 bonds, 3 pseudobonds, 2031 residues, 2 models selected
> select ~sel & ##selected
45035 atoms, 45712 bonds, 6 pseudobonds, 5796 residues, 3 models selected
> hide sel cartoons
> select #9/6:157-198
347 atoms, 351 bonds, 42 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #10/6 to #9/2 & sel pairing ss
No 'to' chains specified
> matchmaker #10/6 & sel to #9/2 & sel pairing ss
No 'to' chains specified
No reference and/or match structure/chain chosen
> matchmaker #10/6 & sel to #9/6 & sel pairing ss
No molecules/chains to match specified
> matchmaker #10/6 to #9/6 & sel pairing ss
Parameters
---
Chain pairing | ss
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 7w1y, chain 6 (#9) with sDH_aligned_12.pdb, chain 6 (#10), sequence
alignment score = 181.4
RMSD between 41 pruned atom pairs is 0.751 angstroms; (across all 42 pairs:
0.835)
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> select #10/6
5334 atoms, 5420 bonds, 1 pseudobond, 670 residues, 2 models selected
> color (#!10 & sel) cornflower blue
> select #10/2:319-373, /6:157-198, /4:296-357
Expected an objects specifier or a keyword
> select #10/2:319-373, #10/6:157-198, #10/4:296-357
Expected an objects specifier or a keyword
> select #10/2:319-373, /6:157-198,4:296-357
Expected an objects specifier or a keyword
> select #10/2:319-373,/6:157-198,4:296-357
Expected an objects specifier or a keyword
> select #10/2:319-373
394 atoms, 403 bonds, 51 residues, 1 model selected
> addcharge #10/6:157-198
> addh #10/6:157-198
Summary of feedback from adding hydrogens to sDH_aligned_12.pdb #10
---
warnings | Not adding hydrogens to sDH_aligned_12.pdb #10/5 GLU 118 CB because
it is missing heavy-atom bond partners
Not adding hydrogens to sDH_aligned_12.pdb #10/5 GLU 119 CB because it is
missing heavy-atom bond partners
Not adding hydrogens to sDH_aligned_12.pdb #10/5 ARG 425 CB because it is
missing heavy-atom bond partners
Not adding hydrogens to sDH_aligned_12.pdb #10/5 ASP 601 CB because it is
missing heavy-atom bond partners
Not adding hydrogens to sDH_aligned_12.pdb #10/5 ARG 602 CB because it is
missing heavy-atom bond partners
333 messages similar to the above omitted
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: sDH_aligned_12.pdb #10/7 PRO 112 N; sDH_aligned_12.pdb #10/F
PRO 112 N
notes | No usable SEQRES records for sDH_aligned_12.pdb (#10) chain 2;
guessing termini instead
No usable SEQRES records for sDH_aligned_12.pdb (#10) chain 3; guessing
termini instead
No usable SEQRES records for sDH_aligned_12.pdb (#10) chain 4; guessing
termini instead
No usable SEQRES records for sDH_aligned_12.pdb (#10) chain 5; guessing
termini instead
No usable SEQRES records for sDH_aligned_12.pdb (#10) chain 6; guessing
termini instead
7 messages similar to the above omitted
Chain-initial residues that are actual N termini: sDH_aligned_12.pdb #10/2 GLU
184, sDH_aligned_12.pdb #10/3 THR 4, sDH_aligned_12.pdb #10/4 VAL 157,
sDH_aligned_12.pdb #10/5 SER 2, sDH_aligned_12.pdb #10/6 ASP 20,
sDH_aligned_12.pdb #10/7 ASP 1, sDH_aligned_12.pdb #10/A GLU 184,
sDH_aligned_12.pdb #10/B THR 4, sDH_aligned_12.pdb #10/C VAL 157,
sDH_aligned_12.pdb #10/D SER 2, sDH_aligned_12.pdb #10/E ASP 20,
sDH_aligned_12.pdb #10/F ASP 1
Chain-initial residues that are not actual N termini: sDH_aligned_12.pdb #10/2
VAL 347, sDH_aligned_12.pdb #10/2 LEU 390, sDH_aligned_12.pdb #10/2 THR 457,
sDH_aligned_12.pdb #10/2 VAL 554, sDH_aligned_12.pdb #10/2 GLU 713,
sDH_aligned_12.pdb #10/3 SER 172, sDH_aligned_12.pdb #10/3 GLU 212,
sDH_aligned_12.pdb #10/3 GLY 254, sDH_aligned_12.pdb #10/3 SER 275,
sDH_aligned_12.pdb #10/3 VAL 563, sDH_aligned_12.pdb #10/3 LEU 739,
sDH_aligned_12.pdb #10/4 HIS 368, sDH_aligned_12.pdb #10/4 PHE 441,
sDH_aligned_12.pdb #10/5 LYS 28, sDH_aligned_12.pdb #10/5 SER 291,
sDH_aligned_12.pdb #10/5 VAL 314, sDH_aligned_12.pdb #10/5 ALA 476,
sDH_aligned_12.pdb #10/5 ILE 504, sDH_aligned_12.pdb #10/5 ILE 554,
sDH_aligned_12.pdb #10/6 VAL 289, sDH_aligned_12.pdb #10/6 GLU 319,
sDH_aligned_12.pdb #10/6 PHE 717, sDH_aligned_12.pdb #10/7 LEU 288,
sDH_aligned_12.pdb #10/7 ARG 321, sDH_aligned_12.pdb #10/7 LEU 410,
sDH_aligned_12.pdb #10/7 LEU 425, sDH_aligned_12.pdb #10/7 THR 473,
sDH_aligned_12.pdb #10/A VAL 347, sDH_aligned_12.pdb #10/A LEU 390,
sDH_aligned_12.pdb #10/A THR 457, sDH_aligned_12.pdb #10/A VAL 554,
sDH_aligned_12.pdb #10/A GLU 713, sDH_aligned_12.pdb #10/B SER 172,
sDH_aligned_12.pdb #10/B GLU 212, sDH_aligned_12.pdb #10/B GLY 254,
sDH_aligned_12.pdb #10/B SER 275, sDH_aligned_12.pdb #10/B VAL 563,
sDH_aligned_12.pdb #10/B LEU 739, sDH_aligned_12.pdb #10/C GLU 232,
sDH_aligned_12.pdb #10/C HIS 368, sDH_aligned_12.pdb #10/C PHE 441,
sDH_aligned_12.pdb #10/D LYS 28, sDH_aligned_12.pdb #10/D SER 291,
sDH_aligned_12.pdb #10/D VAL 314, sDH_aligned_12.pdb #10/D ALA 476,
sDH_aligned_12.pdb #10/D ILE 504, sDH_aligned_12.pdb #10/D ILE 554,
sDH_aligned_12.pdb #10/E ASP 291, sDH_aligned_12.pdb #10/E GLU 319,
sDH_aligned_12.pdb #10/E PHE 717, sDH_aligned_12.pdb #10/F LEU 288,
sDH_aligned_12.pdb #10/F ARG 321, sDH_aligned_12.pdb #10/F LEU 410,
sDH_aligned_12.pdb #10/F LEU 425, sDH_aligned_12.pdb #10/F THR 473
Chain-final residues that are actual C termini: sDH_aligned_12.pdb #10/2 GLN
903, sDH_aligned_12.pdb #10/3 ILE 808, sDH_aligned_12.pdb #10/4 LEU 863,
sDH_aligned_12.pdb #10/6 LEU 787, sDH_aligned_12.pdb #10/7 LEU 640,
sDH_aligned_12.pdb #10/A GLN 903, sDH_aligned_12.pdb #10/B ILE 808,
sDH_aligned_12.pdb #10/C LEU 863, sDH_aligned_12.pdb #10/E LEU 787,
sDH_aligned_12.pdb #10/F LEU 640
Chain-final residues that are not actual C termini: sDH_aligned_12.pdb #10/2
SER 342, sDH_aligned_12.pdb #10/2 VAL 385, sDH_aligned_12.pdb #10/2 LYS 446,
sDH_aligned_12.pdb #10/2 GLN 549, sDH_aligned_12.pdb #10/2 LYS 691,
sDH_aligned_12.pdb #10/3 SER 160, sDH_aligned_12.pdb #10/3 PRO 205,
sDH_aligned_12.pdb #10/3 GLY 246, sDH_aligned_12.pdb #10/3 SER 269,
sDH_aligned_12.pdb #10/3 LEU 520, sDH_aligned_12.pdb #10/3 LYS 656,
sDH_aligned_12.pdb #10/4 GLU 356, sDH_aligned_12.pdb #10/4 THR 424,
sDH_aligned_12.pdb #10/5 LEU 733, sDH_aligned_12.pdb #10/5 PHE 15,
sDH_aligned_12.pdb #10/5 LYS 272, sDH_aligned_12.pdb #10/5 THR 303,
sDH_aligned_12.pdb #10/5 SER 468, sDH_aligned_12.pdb #10/5 ALA 488,
sDH_aligned_12.pdb #10/5 LYS 521, sDH_aligned_12.pdb #10/6 ASP 253,
sDH_aligned_12.pdb #10/6 ASN 307, sDH_aligned_12.pdb #10/6 PRO 662,
sDH_aligned_12.pdb #10/7 GLY 277, sDH_aligned_12.pdb #10/7 LYS 304,
sDH_aligned_12.pdb #10/7 THR 401, sDH_aligned_12.pdb #10/7 LEU 415,
sDH_aligned_12.pdb #10/7 SER 464, sDH_aligned_12.pdb #10/A SER 342,
sDH_aligned_12.pdb #10/A VAL 385, sDH_aligned_12.pdb #10/A LYS 446,
sDH_aligned_12.pdb #10/A GLN 549, sDH_aligned_12.pdb #10/A LYS 691,
sDH_aligned_12.pdb #10/B SER 160, sDH_aligned_12.pdb #10/B PRO 205,
sDH_aligned_12.pdb #10/B GLY 246, sDH_aligned_12.pdb #10/B SER 269,
sDH_aligned_12.pdb #10/B LEU 520, sDH_aligned_12.pdb #10/B LYS 656,
sDH_aligned_12.pdb #10/C PRO 230, sDH_aligned_12.pdb #10/C GLU 356,
sDH_aligned_12.pdb #10/C THR 424, sDH_aligned_12.pdb #10/D LEU 733,
sDH_aligned_12.pdb #10/D PHE 15, sDH_aligned_12.pdb #10/D LYS 272,
sDH_aligned_12.pdb #10/D THR 303, sDH_aligned_12.pdb #10/D SER 468,
sDH_aligned_12.pdb #10/D ALA 488, sDH_aligned_12.pdb #10/D LYS 521,
sDH_aligned_12.pdb #10/E ASP 253, sDH_aligned_12.pdb #10/E ASN 307,
sDH_aligned_12.pdb #10/E PRO 662, sDH_aligned_12.pdb #10/F GLY 277,
sDH_aligned_12.pdb #10/F LYS 304, sDH_aligned_12.pdb #10/F THR 401,
sDH_aligned_12.pdb #10/F LEU 415, sDH_aligned_12.pdb #10/F SER 464
6709 hydrogen bonds
Adding 'H' to sDH_aligned_12.pdb #10/2 VAL 347
Adding 'H' to sDH_aligned_12.pdb #10/2 LEU 390
Adding 'H' to sDH_aligned_12.pdb #10/2 THR 457
Adding 'H' to sDH_aligned_12.pdb #10/2 VAL 554
Adding 'H' to sDH_aligned_12.pdb #10/2 GLU 713
50 messages similar to the above omitted
sDH_aligned_12.pdb #10/3 SER 160 is not terminus, removing H atom from 'C'
sDH_aligned_12.pdb #10/3 PRO 205 is not terminus, removing H atom from 'C'
sDH_aligned_12.pdb #10/3 GLY 246 is not terminus, removing H atom from 'C'
sDH_aligned_12.pdb #10/3 SER 269 is not terminus, removing H atom from 'C'
sDH_aligned_12.pdb #10/3 LYS 656 is not terminus, removing H atom from 'C'
21 messages similar to the above omitted
60220 hydrogens added
Using Amber 20 recommended default charges and atom types for standard
residues
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
sDH_aligned_12.pdb #10: sDH_aligned_12.pdb #10/6 LYS 173: -0.0353 and
sDH_aligned_12.pdb #10/6 ARG 189: -0.0369
> addcharge #10/6:157-198
Using Amber 20 recommended default charges and atom types for standard
residues
1 structure has non-integral total charge.
Details in log.
Here are the structures will non-integral total charge along with the
particular residues from those structures with non-integral total charge:
sDH_aligned_12.pdb #10: sDH_aligned_12.pdb #10/6 LYS 173: -0.0353 and
sDH_aligned_12.pdb #10/6 ARG 189: -0.0369
> select #10/2:319-373
761 atoms, 770 bonds, 51 residues, 1 model selected
> addcharge sel #10/6:157-198
Expected a keyword
> addcharge selection #10/6:157-198
Expected a keyword
> addcharge select #10/6:157-198
Expected a keyword
> addselect #10/6:157-198
Unknown command: addselect #10/6:157-198
> add~select #10/6:157-198
Unknown command: add~select #10/6:157-198
> select add #10/6:157-198
1426 atoms, 1439 bonds, 93 residues, 1 model selected
> select add #10/4:296-357
2381 atoms, 2402 bonds, 154 residues, 1 model selected
> select #10/2
10686 atoms, 10784 bonds, 1 pseudobond, 679 residues, 2 models selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel light salmon
> color sel orange
> color sel navajo white
> color sel bisque
> color sel peach puff
> select #10/4
10225 atoms, 10309 bonds, 1 pseudobond, 682 residues, 2 models selected
> color sel light pink
> color sel lavender blush
[Repeated 1 time(s)]
> color sel light pink
> color sel salmon
> color sel light pink
> select #10/6
10619 atoms, 10705 bonds, 1 pseudobond, 670 residues, 2 models selected
> color sel light sky blue
> color sel cadet blue
> color sel light sky blue
> color sel light blue
> color sel sky blue
> color sel light sky blue
> color sel powder blue
> color sel pale turquoise
> color sel light blue
> hide #!9 models
> select #10
121166 atoms, 122111 bonds, 9 pseudobonds, 7827 residues, 3 models selected
> hide sel cartoons
> select #10/2:319-373
761 atoms, 770 bonds, 51 residues, 1 model selected
> show sel cartoons
> color sel orange
> show sel surfaces
> color (#!10 & sel) orange
> select #10/6:319-373
884 atoms, 892 bonds, 55 residues, 1 model selected
> select #10/6:157-198
665 atoms, 669 bonds, 42 residues, 1 model selected
> show sel surfaces
> color (#!10 & sel) medium blue
> select #10/4:296-357
955 atoms, 963 bonds, 61 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select #10/4:296-357
955 atoms, 963 bonds, 61 residues, 1 model selected
> select #10/4:296-350
846 atoms, 854 bonds, 55 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> select #10/4:296-348
807 atoms, 815 bonds, 53 residues, 1 model selected
> show sel surfaces
> select #10/4:296-350
846 atoms, 854 bonds, 55 residues, 1 model selected
> show sel surfaces
> show sel cartoons
> color (#!10 & sel) magenta
> select #10/5:160-220
967 atoms, 975 bonds, 61 residues, 1 model selected
> show sel surfaces
> show sel cartoons
> color (#!10 & sel) yellow
> show sel cartoons
> select #10/3:138-184
606 atoms, 611 bonds, 36 residues, 1 model selected
> show sel surfaces
> show sel cartoons
> color (#!10 & sel) cyan
> select #10/7:173-227
735 atoms, 737 bonds, 55 residues, 1 model selected
> show sel surfaces
> show sel cartoons
> color (#!10 & sel) forest green
> select #9
66630 atoms, 67929 bonds, 192 pseudobonds, 8266 residues, 4 models selected
> hide #!10 cartoons
> hide #!10 atoms
> hide #!10 surfaces
> show #!10 surfaces
> hide #!10 surfaces
> hide #!10 models
> show #!10 models
> select add #10
187796 atoms, 190040 bonds, 201 pseudobonds, 16093 residues, 21 models
selected
> undo
[Repeated 7 time(s)]Drag select of 258 residues
> show sel surfaces
> select add #10
121166 atoms, 122111 bonds, 9 pseudobonds, 7827 residues, 8 models selected
> select subtract #10
12 models selected
> select add #9
66630 atoms, 67929 bonds, 192 pseudobonds, 8266 residues, 4 models selected
> hide #!10 models
> show #!9 models
> hide sel cartoons
> select #9/2:319-373
432 atoms, 442 bonds, 55 residues, 1 model selected
> show sel surfaces
> select #9/6:157-198
347 atoms, 351 bonds, 42 residues, 1 model selected
> show sel surfaces
> select #9/4:296-350
436 atoms, 444 bonds, 55 residues, 1 model selected
> show sel surfaces
> select #9/3:138-184
379 atoms, 388 bonds, 47 residues, 1 model selected
> show sel surfaces
> color (#!9 & sel) cyan
> select #9/5:160-220
473 atoms, 481 bonds, 61 residues, 1 model selected
> show sel surfaces
> color (#!9 & sel) yellow
> select #9/7:173-227
422 atoms, 430 bonds, 55 residues, 1 model selected
> show sel surfaces
> color (#!9 & sel) forest green
> select clear
> show #!10 models
> hide #!9 models
> show #!9 models
> hide #!10 models
> show #!10 models
> hide #!9 models
> select #10/6:157-198
665 atoms, 669 bonds, 42 residues, 1 model selected
> show sel surfaces
Drag select of sDH_aligned_12.pdb_2 SES surface, 71001 of 831144 triangles,
sDH_aligned_12.pdb_6 SES surface, 61299 of 815316 triangles,
sDH_aligned_12.pdb_4 SES surface, 81610 of 806990 triangles,
sDH_aligned_12.pdb_5 SES surface, 92859 of 790082 triangles,
sDH_aligned_12.pdb_3 SES surface, 56995 of 807602 triangles,
sDH_aligned_12.pdb_7 SES surface, 71476 of 719458 triangles, 258 residues
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
> own/ZF/sDH_aligned_12_2-7_ZF.pdb" models #10 selectedOnly true relModel #10
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
> own/ZF/sDH_aligned_12_2-7_ZF.pdb"
Summary of feedback from opening /Users/fxy/OneDrive - connect.hku.hk/hSH_MS
own/ZF/sDH_aligned_12_2-7_ZF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 GLN 5 32
GLN 5 41 1 10
Start residue of secondary structure not found: HELIX 2 2 LYS 5 54 ASN 5 64 1
11
Start residue of secondary structure not found: HELIX 3 3 MET 5 74 SER 5 79 1
6
Start residue of secondary structure not found: HELIX 4 4 GLU 5 82 LYS 5 90 1
9
Start residue of secondary structure not found: HELIX 5 5 PRO 5 92 VAL 5 110 1
19
299 messages similar to the above omitted
End residue of secondary structure not found: SHEET 7 7 1 LYS 5 220 PHE 5 224
0
Start residue of secondary structure not found: SHEET 8 8 1 THR 5 226 GLN 5
230 0
Start residue of secondary structure not found: SHEET 9 9 1 HIS 5 244 TYR 5
248 0
Start residue of secondary structure not found: SHEET 10 10 1 ARG 5 262 SER 5
270 0
Start residue of secondary structure not found: SHEET 11 11 1 TYR 5 293 VAL 5
301 0
Start residue of secondary structure not found: SHEET 12 12 1 ASN 5 376 LEU 5
380 0
9 messages similar to the above omitted
End residue of secondary structure not found: SHEET 24 24 1 TYR 2 373 GLU 2
380 0
Start residue of secondary structure not found: SHEET 25 25 1 SER 2 393 LEU 2
399 0
Start residue of secondary structure not found: SHEET 26 26 1 GLU 2 413 HIS 2
419 0
Start residue of secondary structure not found: SHEET 27 27 1 VAL 2 438 ALA 2
445 0
Start residue of secondary structure not found: SHEET 28 28 1 ALA 2 543 THR 2
547 0
Start residue of secondary structure not found: SHEET 29 29 1 TYR 2 559 HIS 2
563 0
29 messages similar to the above omitted
End residue of secondary structure not found: SHEET 66 66 1 LYS 4 349 GLN 4
355 0
Start residue of secondary structure not found: SHEET 67 67 1 VAL 4 370 HIS 4
375 0
Start residue of secondary structure not found: SHEET 68 68 1 VAL 4 388 VAL 4
397 0
Start residue of secondary structure not found: SHEET 69 69 1 LYS 4 413 LYS 4
423 0
Start residue of secondary structure not found: SHEET 70 70 1 ILE 4 506 GLY 4
510 0
Start residue of secondary structure not found: SHEET 71 71 1 GLY 4 530 TYR 4
532 0
28 messages similar to the above omitted
End residue of secondary structure not found: SHEET 102 102 1 PHE 7 225 GLN 7
234 0
Start residue of secondary structure not found: SHEET 103 103 1 SER 7 248 GLU
7 254 0
Start residue of secondary structure not found: SHEET 104 104 1 HIS 7 266 ILE
7 272 0
Start residue of secondary structure not found: SHEET 105 105 1 GLU 7 295 LYS
7 301 0
Start residue of secondary structure not found: SHEET 106 106 1 CYS 7 374 GLY
7 377 0
Start residue of secondary structure not found: SHEET 107 107 1 SER 7 397 THR
7 400 0
113 messages similar to the above omitted
Cannot find LINK/SSBOND residue MG (1002 )
Cannot find LINK/SSBOND residue MG (902 )
Cannot find LINK/SSBOND residue MG (902 )
Cannot find LINK/SSBOND residue MG (902 )
Cannot find LINK/SSBOND residue MG (1002 )
1 messages similar to the above omitted
Chain information for sDH_aligned_12_2-7_ZF.pdb #11
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
7 | No description available
> hide #!10 models
> show #!9 models
> hide #11 models
Drag select of 7w1y_2 SES surface, 55248 of 653384 triangles, 7w1y_3 SES
surface, 53931 of 605344 triangles, 7w1y_4 SES surface, 58325 of 591244
triangles, 7w1y_5 SES surface, 68953 of 684272 triangles, 7w1y_6 SES surface,
48362 of 689122 triangles, 7w1y_7 SES surface, 58611 of 601830 triangles
[Repeated 1 time(s)]
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_2-7_ZF.pdb"
> models #9 selectedOnly true relModel #9
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_2-7_ZF.pdb"
[Repeated 1 time(s)]
> hide #!9 models
> show #11 models
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_2-7_ZF.pdb"
> show #!9 models
> hide #11 models
> show #11 models
> hide #11 models
> select clear
Drag select of 7w1y_2 SES surface, 55248 of 653384 triangles, 7w1y_3 SES
surface, 53931 of 605344 triangles, 7w1y_4 SES surface, 58325 of 591244
triangles, 7w1y_5 SES surface, 68953 of 684272 triangles, 7w1y_6 SES surface,
48362 of 689122 triangles, 7w1y_7 SES surface, 58611 of 601830 triangles
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_2-7_ZF.pdb"
> models #9 selectedOnly true relModel #9
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_2-7_ZF.pdb"
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x8' for virtual key 51 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #!9 models
> show #!9 models
> close #9
> show #11 models
> hide #11 models
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_2-7_ZF.pdb"
[Repeated 1 time(s)]
> show #11 models
> select add #11
3915 atoms, 3947 bonds, 258 residues, 1 model selected
> open 7W1Y
Summary of feedback from opening 7W1Y fetched from pdb
---
warnings | Ignoring microheterogeneity for label_seq_id 1 in chain
Ignoring microheterogeneity for label_seq_id 2 in chain S
Ignoring microheterogeneity for label_seq_id 3 in chain S
Ignoring microheterogeneity for label_seq_id 4 in chain S
Ignoring microheterogeneity for label_seq_id 5 in chain S
93 messages similar to the above omitted
7w1y title:
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) [more
info...]
Chain information for 7w1y #9
---
Chain | Description | UniProt
2 A | DNA replication licensing factor MCM2 | MCM2_HUMAN 1-904
3 B | Isoform 2 of DNA replication licensing factor MCM3 | MCM3_HUMAN -44-808
4 C | DNA replication licensing factor MCM4 | MCM4_HUMAN 1-863
5 D | DNA replication licensing factor MCM5 | MCM5_HUMAN 1-734
6 E | DNA replication licensing factor MCM6 | MCM6_HUMAN 1-821
7 F | DNA replication licensing factor MCM7 | MCM7_HUMAN 1-719
O | DNA (49-MER) |
S | DNA (49-MER) |
Non-standard residues in 7w1y #9
---
ADP — adenosine-5'-diphosphate
ATP — adenosine-5'-triphosphate
MG — magnesium ion
ZN — zinc ion
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_2-7_ZF.pdb"
> hide #!9 models
> show #!8 models
> hide #11 models
> hide #!8 models
> show #!3 models
> hide #!3 models
> close #3-8
> show #!9 models
> select #9/2:319-373
432 atoms, 442 bonds, 55 residues, 1 model selected
> select add #9/6:157-198
779 atoms, 793 bonds, 97 residues, 1 model selected
> select add #9/4:296-350
1215 atoms, 1237 bonds, 152 residues, 1 model selected
> select add #9/5:160-220
1688 atoms, 1718 bonds, 213 residues, 1 model selected
> select add #9/3:138-184
2067 atoms, 2106 bonds, 260 residues, 1 model selected
> select add #9/7:173-227
2489 atoms, 2536 bonds, 315 residues, 1 model selected
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_2-7_ZF2.pdb"
> selectedOnly true relModel #9
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_2-7_ZF2.pdb"
Summary of feedback from opening /Users/fxy/OneDrive - connect.hku.hk/hSH_MS
own/ZF/7W1Y_2-7_ZF2.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL 2 203
TYR 2 218 1 16
Start residue of secondary structure not found: HELIX 2 2 SER 2 225 MET 2 237
1 13
Start residue of secondary structure not found: HELIX 3 3 ASN 2 245 SER 2 252
1 8
Start residue of secondary structure not found: HELIX 4 4 LYS 2 253 LYS 2 262
1 10
Start residue of secondary structure not found: HELIX 5 5 CYS 2 263 TYR 2 283
1 21
125 messages similar to the above omitted
End residue of secondary structure not found: HELIX 131 131 CYS 7 211 TYR 7
215 1 5
Start residue of secondary structure not found: HELIX 132 132 ASN 7 336 VAL 7
340 1 5
Start residue of secondary structure not found: HELIX 133 133 PHE 7 363 LYS 7
367 1 5
Start residue of secondary structure not found: HELIX 134 134 ASP 7 396 GLY 7
408 1 13
Start residue of secondary structure not found: HELIX 135 135 ASP 7 409 ILE 7
418 1 10
Start residue of secondary structure not found: HELIX 136 136 ASN 7 425 GLY 7
438 1 14
Start residue of secondary structure not found: HELIX 137 137 ALA 7 465 SER 7
477 1 13
Start residue of secondary structure not found: HELIX 138 138 SER 7 489 THR 7
494 1 6
144 messages similar to the above omitted
Cannot find LINK/SSBOND residue PHE (331 )
Cannot find LINK/SSBOND residue GLN (386 )
Cannot find LINK/SSBOND residue THR (852 )
Cannot find LINK/SSBOND residue SER (855 )
Chain information for 7W1Y_2-7_ZF2.pdb #3
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #11 models
> select #3/2
432 atoms, 442 bonds, 55 residues, 1 model selected
> select add #3/2
432 atoms, 442 bonds, 55 residues, 1 model selected
> color sel orange
> select add #11/2
1193 atoms, 1212 bonds, 106 residues, 2 models selected
> color sel orange
> select #11/3
606 atoms, 611 bonds, 36 residues, 1 model selected
> select add #3/3
985 atoms, 999 bonds, 83 residues, 2 models selected
> color sel cyan
> select add #3/4
1421 atoms, 1443 bonds, 138 residues, 2 models selected
> select #3/4
436 atoms, 444 bonds, 55 residues, 1 model selected
> select add #11/4
1282 atoms, 1298 bonds, 110 residues, 2 models selected
> color sel magenta
> select #11/6
Nothing selected
> select add #3/6
347 atoms, 351 bonds, 42 residues, 1 model selected
> color sel medium blue
> select #11/6
Nothing selected
> hide #3 models
> show #11 cartoons
> hide #11 cartoons
> show #11 surfaces
> hide #!11 surfaces
> close #11
> show #3 models
> select #3/5
473 atoms, 481 bonds, 61 residues, 1 model selected
> color sel yellow
> select #3/7
422 atoms, 430 bonds, 55 residues, 1 model selected
> color sel forest green
> hide #3 models
> show #!10 models
Drag select of sDH_aligned_12.pdb_2 SES surface, 71001 of 831144 triangles,
sDH_aligned_12.pdb_6 SES surface, 61299 of 815316 triangles,
sDH_aligned_12.pdb_4 SES surface, 81610 of 806990 triangles,
sDH_aligned_12.pdb_5 SES surface, 92859 of 790082 triangles,
sDH_aligned_12.pdb_3 SES surface, 56995 of 807602 triangles,
sDH_aligned_12.pdb_7 SES surface, 71476 of 719458 triangles, 258 residues
[Repeated 1 time(s)]
> select add #10/6:157-198
4580 atoms, 669 bonds, 300 residues, 6 models selected
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
> own/ZF/sDH_aligned_12_2-7_ZF.pdb" selectedOnly true relModel #10
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
> own/ZF/sDH_aligned_12_2-7_ZF.pdb"
Summary of feedback from opening /Users/fxy/OneDrive - connect.hku.hk/hSH_MS
own/ZF/sDH_aligned_12_2-7_ZF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL 2 203
TYR 2 218 1 16
Start residue of secondary structure not found: HELIX 2 2 SER 2 225 MET 2 237
1 13
Start residue of secondary structure not found: HELIX 3 3 ASN 2 245 SER 2 252
1 8
Start residue of secondary structure not found: HELIX 4 4 LYS 2 253 LYS 2 262
1 10
Start residue of secondary structure not found: HELIX 5 5 CYS 2 263 TYR 2 283
1 21
277 messages similar to the above omitted
Cannot find LINK/SSBOND residue PHE (331 )
Cannot find LINK/SSBOND residue GLN (386 )
Cannot find LINK/SSBOND residue THR (852 )
Cannot find LINK/SSBOND residue SER (855 )
Chain information for sDH_aligned_12_2-7_ZF.pdb #4
---
Chain | Description
2 | No description available
3 | No description available
4 | No description available
5 | No description available
6 | No description available
7 | No description available
> hide #4 models
> show #3 models
> ui tool show Matchmaker
> hide #!10 models
> show #4 models
> select #4/4
846 atoms, 854 bonds, 55 residues, 1 model selected
> color sel magenta
> select #4/2
761 atoms, 770 bonds, 51 residues, 1 model selected
> color sel orange
> select #4/3
606 atoms, 611 bonds, 36 residues, 1 model selected
> color sel cyan
> select #4/5
967 atoms, 975 bonds, 61 residues, 1 model selected
> color sel yellow
> select #4/6
665 atoms, 669 bonds, 42 residues, 1 model selected
> color sel medium blue
> select #4/4
846 atoms, 854 bonds, 55 residues, 1 model selected
> select #4/7
735 atoms, 737 bonds, 55 residues, 1 model selected
> color sel forest green
> ui tool show Matchmaker
> matchmaker #4/6 to #3/6 pairing ss
Parameters
---
Chain pairing | ss
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 7W1Y_2-7_ZF2.pdb, chain 6 (#3) with sDH_aligned_12_2-7_ZF.pdb,
chain 6 (#4), sequence alignment score = 202.4
RMSD between 41 pruned atom pairs is 0.751 angstroms; (across all 42 pairs:
0.835)
> hide #4 models
> show #4 models
> hide #3 models
> show #3 models
> select add #3
3224 atoms, 3273 bonds, 370 residues, 2 models selected
> select add #4
7069 atoms, 7152 bonds, 615 residues, 2 models selected
> select subtract #4
2489 atoms, 2536 bonds, 315 residues, 1 model selected
> select add #4
7069 atoms, 7152 bonds, 615 residues, 2 models selected
> show sel surfaces
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!3 models
> show #!9 models
> show #!10 models
> select add #10
128235 atoms, 129263 bonds, 9 pseudobonds, 8442 residues, 17 models selected
> show sel & #!10 cartoons
> hide sel & #!10 surfaces
> select subtract #10
7069 atoms, 7152 bonds, 615 residues, 26 models selected
> ui tool show Matchmaker
> matchmaker #9/6 to #2/6 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 6 (#2) with 7w1y, chain 6 (#9), sequence alignment
score = 3078.8
RMSD between 269 pruned atom pairs is 0.685 angstroms; (across all 668 pairs:
11.855)
> matchmaker #10/6 to #2/6 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 6 (#2) with sDH_aligned_12.pdb, chain 6 (#10),
sequence alignment score = 3389.1
RMSD between 668 pruned atom pairs is 0.338 angstroms; (across all 668 pairs:
0.338)
> select subtract #4
2489 atoms, 2536 bonds, 315 residues, 13 models selected
> select subtract #3
6 models selected
> select add #9
66630 atoms, 67929 bonds, 192 pseudobonds, 8266 residues, 4 models selected
> show sel cartoons
> hide sel surfaces
> select add #10
187796 atoms, 190040 bonds, 201 pseudobonds, 16093 residues, 7 models selected
> select subtract #10
66630 atoms, 67929 bonds, 192 pseudobonds, 8266 residues, 16 models selected
> select subtract #9
Nothing selected
> select add #9
66630 atoms, 67929 bonds, 192 pseudobonds, 8266 residues, 4 models selected
> hide sel atoms
> select subtract #9
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!10 models
> color #9 #c0f4e7ff
> color #9 #caeef4ff
> ui tool show Matchmaker
> matchmaker #9/3 to #2/3 pairing ss
Parameters
---
Chain pairing | ss
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 hMCM-SH-18-4-2-coot-9(clash score 18_for M3CTE-MCM2
interaction).pdb, chain 3 (#2) with 7w1y, chain 3 (#9), sequence alignment
score = 2547
RMSD between 241 pruned atom pairs is 1.069 angstroms; (across all 538 pairs:
13.658)
> hide #!2 models
> hide #!9 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!4 models
> ui tool show Matchmaker
> matchmaker #3/3 to #4/3 pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12_2-7_ZF.pdb, chain 3 (#4) with 7W1Y_2-7_ZF2.pdb,
chain 3 (#3), sequence alignment score = 144.8
RMSD between 34 pruned atom pairs is 0.604 angstroms; (across all 36 pairs:
2.154)
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!2 models
> hide #!2 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!9 models
> ui tool show Matchmaker
> matchmaker #9/3 to #3/3 pairing ss
Parameters
---
Chain pairing | ss
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 7W1Y_2-7_ZF2.pdb, chain 3 (#3) with 7w1y, chain 3 (#9), sequence
alignment score = 223.9
RMSD between 47 pruned atom pairs is 0.000 angstroms; (across all 47 pairs:
0.000)
> select #9/G-H
Nothing selected
> select #9/O-S
2009 atoms, 2252 bonds, 95 pseudobonds, 98 residues, 2 models selected
> select clear
> select #9/O-S
2009 atoms, 2252 bonds, 95 pseudobonds, 98 residues, 2 models selected
> select ~sel & ##selected
64621 atoms, 65677 bonds, 97 pseudobonds, 8168 residues, 3 models selected
> hide sel cartoons
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!10 models
> ui tool show Matchmaker
> matchmaker #10/3 to #3/3 pairing ss
Parameters
---
Chain pairing | ss
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 7W1Y_2-7_ZF2.pdb, chain 3 (#3) with sDH_aligned_12.pdb, chain 3
(#10), sequence alignment score = 132.8
RMSD between 34 pruned atom pairs is 0.604 angstroms; (across all 36 pairs:
2.154)
> 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
> select #10/B:319-373
799 atoms, 802 bonds, 55 residues, 1 model selected
> select add #10/c:138-184
1238 atoms, 1244 bonds, 83 residues, 2 models selected
> select add #10/C:138-184
1238 atoms, 1244 bonds, 83 residues, 3 models selected
> select add #10/D:296-350
1933 atoms, 1943 bonds, 128 residues, 3 models selected
> select clear
> select #10/A:319-373
761 atoms, 770 bonds, 51 residues, 1 model selected
> select #10/B:138-184
606 atoms, 611 bonds, 36 residues, 1 model selected
> select add #10/A:319-373
1367 atoms, 1381 bonds, 87 residues, 2 models selected
> select add #10/C:296-350
2213 atoms, 2235 bonds, 142 residues, 3 models selected
> select add #10/D:160-220
3180 atoms, 3210 bonds, 203 residues, 4 models selected
> select add #10/E:157-198
3845 atoms, 3879 bonds, 245 residues, 5 models selected
> select add #10/F:173-227
4550 atoms, 4587 bonds, 300 residues, 6 models selected
> show sel surfaces
> select ~sel & ##selected
116616 atoms, 117524 bonds, 9 pseudobonds, 7527 residues, 3 models selected
> hide sel cartoons
> show #!4 models
> hide #!9 models
> hide #!3 models
> show #!9 models
> select #10/F:173-227
705 atoms, 708 bonds, 55 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #3/5 to #9/5 pairing ss
Parameters
---
Chain pairing | ss
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 7w1y, chain 5 (#9) with 7W1Y_2-7_ZF2.pdb, chain 5 (#3), sequence
alignment score = 288.4
RMSD between 61 pruned atom pairs is 0.000 angstroms; (across all 61 pairs:
0.000)
> matchmaker #4/5 to #9/5 pairing ss
Parameters
---
Chain pairing | ss
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 7w1y, chain 5 (#9) with sDH_aligned_12_2-7_ZF.pdb, chain 5 (#4),
sequence alignment score = 288.4
RMSD between 53 pruned atom pairs is 1.067 angstroms; (across all 61 pairs:
1.309)
> matchmaker #10/5 to #9/5 pairing ss
Parameters
---
Chain pairing | ss
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 7w1y, chain 5 (#9) with sDH_aligned_12.pdb, chain 5 (#10), sequence
alignment score = 2766.1
RMSD between 136 pruned atom pairs is 0.905 angstroms; (across all 633 pairs:
20.197)
> view
> show #!3 models
> color (#!10 & sel) forest green
> select #10/A:319-373
761 atoms, 770 bonds, 51 residues, 1 model selected
> color (#!10 & sel) orange
> select #10/B:138-184
606 atoms, 611 bonds, 36 residues, 1 model selected
> color (#!10 & sel) cyan
> hide #!3 models
> hide #!4 models
> show #!4 models
> select #9/D:160-220
467 atoms, 475 bonds, 61 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #10/D to #9/D & sel pairing ss
Parameters
---
Chain pairing | ss
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 7w1y, chain D (#9) with sDH_aligned_12.pdb, chain D (#10), sequence
alignment score = 305.8
RMSD between 54 pruned atom pairs is 1.101 angstroms; (across all 61 pairs:
1.882)
> select #10/D:160-220
967 atoms, 975 bonds, 61 residues, 1 model selected
> color (#!10 & sel) yellow
> select #10/E:157-198
665 atoms, 669 bonds, 42 residues, 1 model selected
> color (#!10 & sel) medium blue
> select #10/C:296-357
955 atoms, 963 bonds, 61 residues, 1 model selected
> color (#!10 & sel) magenta
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/ZF comparison.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 641, in save
fserialize(stream, data)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 147, in write
self._f.write(buf)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save '/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/ZF
comparison.cxs': [Errno 28] No space left on device
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/ZF_comparison.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 641, in save
fserialize(stream, data)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 147, in write
self._f.write(buf)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save '/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
own/ZF/ZF_comparison.cxs': [Errno 28] No space left on device
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/ZF_comparison.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 641, in save
fserialize(stream, data)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 147, in write
self._f.write(buf)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save '/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
own/ZF/ZF_comparison.cxs': [Errno 28] No space left on device
> select add #10
121166 atoms, 122111 bonds, 9 pseudobonds, 7827 residues, 4 models selected
> select subtract #10
12 models selected
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/zf_comparision.cxs"
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 912, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/session.py", line 641, in save
fserialize(stream, data)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/serialize.py", line 76, in msgpack_serialize
stream.write(packer.pack(obj))
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/safesave.py", line 147, in write
self._f.write(buf)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
OSError: [Errno 28] No space left on device
OSError: [Errno 28] No space left on device
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/lz4/frame/__init__.py", line 741, in write
self._fp.write(compressed)
See log for complete Python traceback.
Cannot save '/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
own/ZF/zf_comparision.cxs': [Errno 28] No space left on device
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/ZF_comparison.cxs"
——— End of log from Thu May 16 16:03:08 2024 ———
opened ChimeraX session
> select #12/5:160-220 #12/D:160-220
Nothing selected
> select #10/5:160-220 #10/D:160-220
1934 atoms, 1950 bonds, 122 residues, 1 model selected
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/sDH_aligned_12_A-
> F_ZF.pdb"
Summary of feedback from opening /Users/fxy/OneDrive - connect.hku.hk/hSH_MS
own/ZF/sDH_aligned_12_A-F_ZF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL 2 203
TYR 2 218 1 16
Start residue of secondary structure not found: HELIX 2 2 SER 2 225 MET 2 237
1 13
Start residue of secondary structure not found: HELIX 3 3 ASN 2 245 SER 2 252
1 8
Start residue of secondary structure not found: HELIX 4 4 LYS 2 253 LYS 2 262
1 10
Start residue of secondary structure not found: HELIX 5 5 CYS 2 263 TYR 2 283
1 21
277 messages similar to the above omitted
Cannot find LINK/SSBOND residue PHE (331 )
Cannot find LINK/SSBOND residue GLN (386 )
Cannot find LINK/SSBOND residue THR (852 )
Cannot find LINK/SSBOND residue SER (855 )
Chain information for sDH_aligned_12_A-F_ZF.pdb #5
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> ui tool show Matchmaker
> matchmaker #5/D to #10/D & sel pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain D (#10) with sDH_aligned_12_A-F_ZF.pdb,
chain D (#5), sequence alignment score = 291.4
RMSD between 61 pruned atom pairs is 0.000 angstroms; (across all 61 pairs:
0.000)
> matchmaker #9/D to #10/D & sel pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain D (#10) with 7w1y, chain D (#9), sequence
alignment score = 305.8
RMSD between 54 pruned atom pairs is 1.101 angstroms; (across all 61 pairs:
1.882)
> matchmaker #9/5 to #10/5 & sel pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain 5 (#10) with 7w1y, chain 5 (#9), sequence
alignment score = 300.4
RMSD between 53 pruned atom pairs is 1.067 angstroms; (across all 61 pairs:
1.309)
> matchmaker #4/5 to #10/5 & sel pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain 5 (#10) with sDH_aligned_12_2-7_ZF.pdb,
chain 5 (#4), sequence alignment score = 291.4
RMSD between 61 pruned atom pairs is 0.000 angstroms; (across all 61 pairs:
0.000)
> hide #!10 models
> select add #5
6484 atoms, 6537 bonds, 422 residues, 4 models selected
> select add #10
125716 atoms, 126698 bonds, 9 pseudobonds, 8127 residues, 6 models selected
> select subtract #10
4550 atoms, 4587 bonds, 300 residues, 13 models selected
> show sel surfaces
> hide sel cartoons
> hide sel atoms
> select add #3
7039 atoms, 7123 bonds, 615 residues, 8 models selected
> select subtract #5
2489 atoms, 2536 bonds, 315 residues, 13 models selected
> ui tool show Matchmaker
> matchmaker #3/5 to #10/5 & sel pairing ss
No 'to' chains specified
> matchmaker #3/5 to #10/5 pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain 5 (#10) with 7W1Y_2-7_ZF2.pdb, chain 5
(#3), sequence alignment score = 291.4
RMSD between 53 pruned atom pairs is 1.067 angstroms; (across all 61 pairs:
1.309)
> show #!3 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> show #!10 models
> select add #9
69119 atoms, 70465 bonds, 192 pseudobonds, 8581 residues, 11 models selected
> select add #10
190285 atoms, 192576 bonds, 201 pseudobonds, 16408 residues, 14 models
selected
> show sel & #!9-10 cartoons
> hide sel & #!9-10 surfaces
> select subtract #9
123655 atoms, 124647 bonds, 9 pseudobonds, 8142 residues, 22 models selected
> select subtract #10
2489 atoms, 2536 bonds, 315 residues, 19 models selected
> ui tool show Matchmaker
> matchmaker #9/3 to #10/3 pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
> select #10/3 #10/B
20240 atoms, 20374 bonds, 1306 residues, 1 model selected
> color (#!10 & sel) cyan
> select #9/3 #9/B
10244 atoms, 10404 bonds, 8 pseudobonds, 1305 residues, 3 models selected
> color (#!9 & sel) cornflower blue
> ui tool show Matchmaker
> matchmaker #!9 to #10
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 sDH_aligned_12.pdb, chain 2 (#10) with 7w1y, chain 2 (#9), sequence
alignment score = 3152.3
RMSD between 340 pruned atom pairs is 0.848 angstroms; (across all 677 pairs:
18.086)
> matchmaker #!9 to #10/3 pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
> matchmaker #!9 to #10/3 pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
> matchmaker #!9 to #10 & sel showAlignment true
No 'to' model specified
> select #10/3 #10/B
20240 atoms, 20374 bonds, 1306 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!9 to #10 & sel showAlignment true
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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: 7w1y #9/3, sDH_aligned_12.pdb
#10/3
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
> matchmaker #!9 to #10 & sel showAlignment true
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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: 7w1y #9/3, sDH_aligned_12.pdb
#10/3
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
> matchmaker #!9 to #10 & sel showAlignment true
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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
Alignment identifier is 3
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3
Hiding conservation header for alignment 3
Chains used in RMSD evaluation for alignment 3: 7w1y #9/3, sDH_aligned_12.pdb
#10/3
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
> select #10/3 #10/B #9/3 #9/B
30484 atoms, 30778 bonds, 8 pseudobonds, 2611 residues, 4 models selected
> ui tool show Matchmaker
[Repeated 1 time(s)]
> matchmaker #!9 & sel to #10 & 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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
> matchmaker #!9 & sel to #10 & 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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
> matchmaker #!9 & sel to #10 & 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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
RMSD between 205 pruned atom pairs is 1.085 angstroms; (across all 582 pairs:
14.545)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> mmaker #9/3,B to #12/3,B pair ss
No 'to' chains specified
> select add #9
86870 atoms, 88303 bonds, 192 pseudobonds, 9572 residues, 7 models selected
> select subtract #9
20240 atoms, 20374 bonds, 1306 residues, 3 models selected
> select add #10
121166 atoms, 122111 bonds, 9 pseudobonds, 7827 residues, 5 models selected
> select subtract #10
12 models selected
> mmaker #9/3,B to #12/3,B pair ss
No 'to' chains specified
> mmaker #9/3,B to #10/3,B pair ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain 3 (#10) with 7w1y, chain 3 (#9), sequence
alignment score = 2746.1
Matchmaker sDH_aligned_12.pdb, chain B (#10) with 7w1y, chain B (#9), sequence
alignment score = 2720.3
RMSD between 338 pruned atom pairs is 1.300 angstroms; (across all 1164 pairs:
17.249)
> ui tool show Matchmaker
> matchmaker #4/3 to #10/3 pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain 3 (#10) with sDH_aligned_12_2-7_ZF.pdb,
chain 3 (#4), sequence alignment score = 170.6
RMSD between 36 pruned atom pairs is 0.000 angstroms; (across all 36 pairs:
0.000)
> show #!3 models
> hide #!9 models
> hide #!3 models
> show #!4 models
> show #!5 models
> ui tool show Matchmaker
> matchmaker #5/B to #10/B pairing ss
Parameters
---
Chain pairing | ss
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 sDH_aligned_12.pdb, chain B (#10) with sDH_aligned_12_A-F_ZF.pdb,
chain B (#5), sequence alignment score = 170.6
RMSD between 36 pruned atom pairs is 0.000 angstroms; (across all 36 pairs:
0.000)
> show #!3 models
> ui tool show Matchmaker
[Repeated 1 time(s)]
> open "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/7W1Y_A-F_ZF.pdb"
Summary of feedback from opening /Users/fxy/OneDrive - connect.hku.hk/hSH_MS
own/ZF/7W1Y_A-F_ZF.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 VAL 2 203
TYR 2 218 1 16
Start residue of secondary structure not found: HELIX 2 2 SER 2 225 MET 2 237
1 13
Start residue of secondary structure not found: HELIX 3 3 ASN 2 245 SER 2 252
1 8
Start residue of secondary structure not found: HELIX 4 4 LYS 2 253 LYS 2 262
1 10
Start residue of secondary structure not found: HELIX 5 5 CYS 2 263 TYR 2 283
1 21
277 messages similar to the above omitted
Cannot find LINK/SSBOND residue PHE (331 )
Cannot find LINK/SSBOND residue GLN (386 )
Cannot find LINK/SSBOND residue THR (852 )
Cannot find LINK/SSBOND residue SER (855 )
Chain information for 7W1Y_A-F_ZF.pdb #6
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> ui tool show Matchmaker
> matchmaker #6/B to #9/B pairing ss
Parameters
---
Chain pairing | ss
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 7w1y, chain B (#9) with 7W1Y_A-F_ZF.pdb, chain B (#6), sequence
alignment score = 222.7
RMSD between 47 pruned atom pairs is 0.000 angstroms; (across all 47 pairs:
0.000)
> hide #6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> select add #6
2483 atoms, 2530 bonds, 315 residues, 1 model selected
> show #!10 surfaces
> undo
> select subtract #6
Nothing selected
> select add #6
2483 atoms, 2530 bonds, 315 residues, 1 model selected
> show #6 models
> show sel surfaces
> hide sel cartoons
> hide sel atoms
> hide #!10 models
> show #!4 models
> show #!5 models
> show #!3 models
> hide #!4 models
> hide #!5 models
> help help:user/preferences.html#startup
> select #3/3 #3/B #4/3 #4/B #5/3 #5/B #6/3 #6/B
1970 atoms, 1998 bonds, 166 residues, 4 models selected
> color (#!3,6 & sel) cyan
> select #3/4 #3/C #4/4 #4/C #5/4 #5/C #6/4 #6/C
2564 atoms, 2596 bonds, 220 residues, 4 models selected
> color (#!3,6 & sel) magenta
> select #3/2 #3/A #4/2 #4/A #5/2 #5/A #6/2 #6/A
2386 atoms, 2424 bonds, 212 residues, 4 models selected
> color (#!3,6 & sel) orange
> select #3/5 #3/D #4/5 #4/D #5/5 #5/D #6/5 #6/D
2874 atoms, 2906 bonds, 244 residues, 4 models selected
> color (#!3,6 & sel) yellow
> select #3/6 #3/E #4/6 #4/E #5/6 #5/E #6/6 #6/E
2024 atoms, 2040 bonds, 168 residues, 4 models selected
> color (#!3,6 & sel) blue
> select #3/7 #3/F #4/7 #4/F #5/7 #5/F #6/7 #6/F
2284 atoms, 2305 bonds, 220 residues, 4 models selected
> color (#!3,6 & sel) forest green
> hide #!3 models
> hide #!6 models
> show #!4 models
> show #!5 models
> color (#!4-5 & sel) forest green
> select #5/6 #5/E
665 atoms, 669 bonds, 42 residues, 1 model selected
> color (#!5 & sel) blue
> select #5/5 #5/D
967 atoms, 975 bonds, 61 residues, 1 model selected
> color (#!5 & sel) yellow
> select #5/4 #5/C
846 atoms, 854 bonds, 55 residues, 1 model selected
> color (#!5 & sel) magenta
> select #5/3 #5/B
606 atoms, 611 bonds, 36 residues, 1 model selected
> color (#!5 & sel) cyan
> select #5/2 #5/A
761 atoms, 770 bonds, 51 residues, 1 model selected
> color (#!5 & sel) orange
> hide #!5 models
> show #!3 models
> select #3/2
432 atoms, 442 bonds, 55 residues, 1 model selected
> color (#!3 & sel) lime
> select #3/3
379 atoms, 388 bonds, 47 residues, 1 model selected
> ui tool show "Color Actions"
> color sel azure
> color sel light cyan
> color sel powder blue
> select #3/2
432 atoms, 442 bonds, 55 residues, 1 model selected
> ui tool show "Color Actions"
> color sel lemon chiffon
> color sel light goldenrod yellow
> color sel wheat
> color sel peach puff
> color sel moccasin
> color sel cornsilk
> color sel light goldenrod yellow
> select #3/4
436 atoms, 444 bonds, 55 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pink
> color sel light pink
[Repeated 1 time(s)]
> select #3/5
473 atoms, 481 bonds, 61 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale goldenrod
> color sel lemon chiffon
> select #3/2
432 atoms, 442 bonds, 55 residues, 1 model selected
> ui tool show "Color Actions"
> color sel navajo white
[Repeated 1 time(s)]
> color sel peach puff
> color sel navajo white
> select #3/
Expected an objects specifier or a keyword
> select #3/6
347 atoms, 351 bonds, 42 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light blue
> color sel light sky blue
> select #3/7
422 atoms, 430 bonds, 55 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark sea green
> select add #3
2489 atoms, 2536 bonds, 315 residues, 2 models selected
> select subtract #3
6 models selected
> select add #3
2489 atoms, 2536 bonds, 315 residues, 1 model selected
> graphics silhouettes true
> lighting flat
> set bgColor white
> set bgColor #ffffff00
> select subtract #3
6 models selected
> set bgColor black
> set bgColor transparent
> hide #!4 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!3 models
> show #!4 models
> lighting full
> lighting soft
> graphics silhouettes false
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> select #3/2
432 atoms, 442 bonds, 55 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light salmon
> select #3/3
379 atoms, 388 bonds, 47 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale turquoise
> color sel powder blue
> color sel pale turquoise
> select #3/5
473 atoms, 481 bonds, 61 residues, 1 model selected
> ui tool show "Color Actions"
> color sel pale goldenrod
> select #3/6
347 atoms, 351 bonds, 42 residues, 1 model selected
> color (#!3 & sel) cornflower blue
> select add #3
2489 atoms, 2536 bonds, 315 residues, 2 models selected
> select subtract #3
6 models selected
> select #3/7
422 atoms, 430 bonds, 55 residues, 1 model selected
> select #3/3
379 atoms, 388 bonds, 47 residues, 1 model selected
> ui tool show "Color Actions"
> color sel sky blue
> color sel light sky blue
> color sel light blue
> color sel light sky blue
> color sel sky blue
> color sel light sky blue
[Repeated 1 time(s)]
> select add #3
2489 atoms, 2536 bonds, 315 residues, 2 models selected
> select subtract #3
6 models selected
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> show #!4 models
> hide #!3 models
> ui tool show "Side View"
> set bgColor white
> set bgColor #ffffff00
> hide #!4 models
> show #!3 models
> show #!9 models
> hide #!9 models
> show #!4 models
> hide #!3 models
> ui tool show "Color Actions"
> show #!3 models
> hide #!4 models
> show #!9 models
> hide #!9 models
> show #!4 models
> hide #!3 models
Mismatch between Cocoa '\x0' and Carbon 'l' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'L' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'l' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'l' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ac' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d2' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00ac' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d2' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xc' for virtual key 37 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> lighting brightness 1
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting brightness flat 1
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting brightness flat1
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting brightness [1]
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting brightness [1.0]
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting brightness=1.0
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting brightness
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting brightness
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting brightness 3
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> show #!5 models
> hide #!5 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> select #3/2
432 atoms, 442 bonds, 55 residues, 1 model selected
> color (#!3 & sel) #7dfa5aff
> color (#!3 & sel) #7b7b7bff
> color (#!3 & sel) #80fb5fff
> select #3/3
379 atoms, 388 bonds, 47 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!3 & sel) #b39059ff
> select #3/4
436 atoms, 444 bonds, 55 residues, 1 model selected
> color (#!3 & sel) #e4cc69ff
> select #3/5
473 atoms, 481 bonds, 61 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!3 & sel) #d3d3d4ff
> color (#!3 & sel) dark gray
> select #3/6
347 atoms, 351 bonds, 42 residues, 1 model selected
> color (#!3 & sel) #f2acd9ff
> select #3/7
422 atoms, 430 bonds, 55 residues, 1 model selected
> color (#!3 & sel) #a5a6d6ff
> select #3/2
432 atoms, 442 bonds, 55 residues, 1 model selected
> color (#!3 & sel) #66dc42ff
> hide #!3 models
> show #!3 models
> select add #3
2489 atoms, 2536 bonds, 315 residues, 2 models selected
> select subtract #3
6 models selected
> ui tool show Matchmaker
> select #3/3
379 atoms, 388 bonds, 47 residues, 1 model selected
> color (#!3 & sel) #68e143ff
> color (#!3 & sel) #68e145ff
> color (#!3 & sel) #68e044ff
> color (#!3 & sel) #67de44ff
> color (#!3 & sel) #66dc43ff
[Repeated 1 time(s)]
> color (#!3 & sel) #65db43ff
[Repeated 1 time(s)]
> color (#!3 & sel) #65da42ff
> color (#!3 & sel) #64d942ff
[Repeated 1 time(s)]
> color (#!3 & sel) #64d842ff
> color (#!3 & sel) #63d741ff
> color (#!3 & sel) #63d641ff
[Repeated 1 time(s)]
> color (#!3 & sel) #63d541ff
[Repeated 1 time(s)]
> color (#!3 & sel) #62d541ff
> color (#!3 & sel) #62d441ff
[Repeated 1 time(s)]
> undo
[Repeated 1 time(s)]
> color (#!3 & sel) #b29159ff
> color (#!3 & sel) #b2915aff
> color (#!3 & sel) #b2925aff
> color (#!3 & sel) #b3925aff
> color (#!3 & sel) #b4935bff
> color (#!3 & sel) #b5945bff
> color (#!3 & sel) #b7955cff
> color (#!3 & sel) #b8965cff
> color (#!3 & sel) #ba985eff
> color (#!3 & sel) #bb985eff
> color (#!3 & sel) #bb995eff
> color (#!3 & sel) #bc995fff
> color (#!3 & sel) #bc9a5fff
[Repeated 1 time(s)]
> color (#!3 & sel) #bd9a5fff
[Repeated 1 time(s)]
> color (#!3 & sel) #bd9b5fff
> color (#!3 & sel) #be9b60ff
[Repeated 1 time(s)]
> select #3/2
432 atoms, 442 bonds, 55 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!3 & sel) #00f900ff
> color (#!3 & sel) #91ff5fff
> color (#!3 & sel) #00f900ff
> color (#!3 & sel) #72f54bff
> color (#!3 & sel) #71f54bff
> color (#!3 & sel) #71f34aff
> color (#!3 & sel) #70f24aff
> color (#!3 & sel) #6ff049ff
> color (#!3 & sel) #6fef49ff
[Repeated 1 time(s)]
> color (#!3 & sel) #6eef49ff
> color (#!3 & sel) #6eee49ff
[Repeated 1 time(s)]
> color (#!3 & sel) #6eed48ff
[Repeated 1 time(s)]
> color (#!3 & sel) #6dec48ff
> color (#!3 & sel) #6deb48ff
> color (#!3 & sel) #6cea47ff
[Repeated 1 time(s)]
> color (#!3 & sel) #6be847ff
[Repeated 2 time(s)]
> color (#!3 & sel) #6be747ff
> color (#!3 & sel) #6be746ff
[Repeated 1 time(s)]
> color (#!3 & sel) #6ae546ff
> color (#!3 & sel) #6ae446ff
> color (#!3 & sel) #69e345ff
[Repeated 1 time(s)]
> color (#!3 & sel) #69e245ff
> color (#!3 & sel) #68e145ff
[Repeated 2 time(s)]
> color (#!3 & sel) #69e245ff
[Repeated 1 time(s)]
> color (#!3 & sel) #69e345ff
[Repeated 1 time(s)]
> color (#!3 & sel) #69e445ff
> color (#!3 & sel) #6ae446ff
> color (#!3 & sel) #6ae546ff
> color (#!3 & sel) #6ae646ff
> color (#!3 & sel) #6be646ff
> color (#!3 & sel) #6be746ff
> color (#!3 & sel) #6be747ff
> select add #3
2489 atoms, 2536 bonds, 315 residues, 2 models selected
> select subtract #3
6 models selected
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!9 models
> hide #!9 models
> ui tool show "Side View"
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!9 models
> hide #!9 models
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
> own/ZF/DH2-7_ZF_bottom.tif" width 688 height 634 supersample 3
> transparentBackground true
> hide #!3 models
> show #!2 models
> hide #!2 models
> show #!4 models
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
> own/ZF/sDH2-7_ZF_bottom.tif" width 688 height 634 supersample 3
> transparentBackground true
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> turn y 90
> turn y -90
> turn x 90
> hide #!3 models
> show #!3 models
> hide #!4 models
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/DH2-7_ZF_side.tif"
> width 688 height 634 supersample 3 transparentBackground true
> show #!4 models
> hide #!3 models
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/sDH2-7_ZF_side.tif"
> width 688 height 634 supersample 3 transparentBackground true
> show #!3 models
> show #!5 models
> hide #!3 models
> turn y 90
> turn y -90
[Repeated 1 time(s)]
> hide #!4 models
> hide #!5 models
> show #!6 models
> show #!3 models
> help help:user/preferences.html#startup
> select #6/B
379 atoms, 388 bonds, 47 residues, 1 model selected
> hide #!3 models
> show #!3 models
> hide #!6 models
> show #!6 models
> color (#!6 & sel) #cdaa73ff
> select #6/D
467 atoms, 475 bonds, 61 residues, 1 model selected
> color (#!6 & sel) dark gray
> select #6/D,b
846 atoms, 863 bonds, 108 residues, 1 model selected
> select ~sel & ##selected
1637 atoms, 1667 bonds, 207 residues, 1 model selected
> hide sel surfaces
> select #3/3,5
852 atoms, 869 bonds, 108 residues, 1 model selected
> select ~sel & ##selected
1637 atoms, 1667 bonds, 207 residues, 1 model selected
> hide sel surfaces
> hide sel cartoons
> hide sel atoms
> show #!4 models
> hide #!3 models
> hide #!6 models
> select #4/3,5
1573 atoms, 1586 bonds, 97 residues, 1 model selected
> select ~sel & ##selected
3007 atoms, 3030 bonds, 203 residues, 1 model selected
> hide sel surfaces
> hide sel atoms
> show #!5 models
> select #5/B/D
1573 atoms, 1586 bonds, 97 residues, 1 model selected
> select ~sel & ##selected
2977 atoms, 3001 bonds, 203 residues, 1 model selected
> hide sel surfaces
> show #!6 models
> show #!3 models
> hide #!3 models
> hide #!6 models
> show #!6 models
> show #!3 models
Drag select of 7W1Y_2-7_ZF2.pdb_3 SES surface, 7W1Y_2-7_ZF2.pdb_5 SES surface,
sDH_aligned_12_2-7_ZF.pdb_3 SES surface, sDH_aligned_12_2-7_ZF.pdb_5 SES
surface, sDH_aligned_12_A-F_ZF.pdb_B SES surface, sDH_aligned_12_A-F_ZF.pdb_D
SES surface, 7W1Y_A-F_ZF.pdb_B SES surface, 7W1Y_A-F_ZF.pdb_D SES surface,
2425 atoms
[Repeated 1 time(s)]
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> hide sel surfaces
[Repeated 1 time(s)]
> select #6/D:192@CB
1 atom, 1 residue, 1 model selected
> select add #5/D:193@CD2
2 atoms, 2 residues, 3 models selected
> select #5/D:189@HA
1 atom, 1 residue, 1 model selected
Drag select of sDH_aligned_12_A-F_ZF.pdb_B SES surface, sDH_aligned_12_A-
F_ZF.pdb_D SES surface, 7W1Y_A-F_ZF.pdb_B SES surface, 7W1Y_A-F_ZF.pdb_D SES
surface, 205 residues
Drag select of sDH_aligned_12_A-F_ZF.pdb_B SES surface, sDH_aligned_12_A-
F_ZF.pdb_D SES surface, 7W1Y_A-F_ZF.pdb_B SES surface, 7W1Y_A-F_ZF.pdb_D SES
surface, 194 residues
> hide sel cartoons
> show sel cartoons
> hide sel surfaces
[Repeated 1 time(s)]
> select add #6
4780 atoms, 2530 bonds, 509 residues, 11 models selected
> select subtract #6
2297 atoms, 194 residues, 14 models selected
> select add #5
6847 atoms, 4587 bonds, 494 residues, 9 models selected
> select subtract #5
2297 atoms, 194 residues, 12 models selected
> select add #4
5393 atoms, 4616 bonds, 403 residues, 6 models selected
> select subtract #4
813 atoms, 103 residues, 9 models selected
> select add #3
2489 atoms, 2536 bonds, 315 residues, 3 models selected
> select subtract #3
6 models selected
> select add #4
4580 atoms, 4616 bonds, 300 residues, 1 model selected
> select subtract #4
6 models selected
> select add #3
2489 atoms, 2536 bonds, 315 residues, 1 model selected
> select subtract #3
6 models selected
> select add #5
4550 atoms, 4587 bonds, 300 residues, 1 model selected
> hide sel surfaces
> show sel cartoons
> select #5/B/D
1573 atoms, 1586 bonds, 97 residues, 1 model selected
> select ~sel & ##selected
2977 atoms, 3001 bonds, 203 residues, 1 model selected
> hide sel cartoons
> select add #6
5460 atoms, 5531 bonds, 518 residues, 6 models selected
> hide sel surfaces
> show sel cartoons
> select #6/B,D
846 atoms, 863 bonds, 108 residues, 1 model selected
> select ~sel & ##selected
1637 atoms, 1667 bonds, 207 residues, 1 model selected
> hide sel cartoons
> undo
> select #6/B,D
846 atoms, 863 bonds, 108 residues, 1 model selected
> select ~sel & ##selected
1637 atoms, 1667 bonds, 207 residues, 1 model selected
> hide sel cartoons
> select add #3
4126 atoms, 4203 bonds, 522 residues, 6 models selected
> select subtract #3
1637 atoms, 1667 bonds, 207 residues, 11 models selected
> select add #4
6217 atoms, 6283 bonds, 507 residues, 6 models selected
> select subtract #4
1637 atoms, 1667 bonds, 207 residues, 11 models selected
> select add #5
6187 atoms, 6254 bonds, 507 residues, 6 models selected
> select #5/B,D
1573 atoms, 1586 bonds, 97 residues, 1 model selected
> select ~sel & ##selected
2977 atoms, 3001 bonds, 203 residues, 1 model selected
> hide sel cartoons
> show #!9 models
> view orient
[Repeated 1 time(s)]
> view
> view orient
[Repeated 1 time(s)]
Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'T' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 't' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2020' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02c7' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2020' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02c7' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x14' for virtual key 17 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> turn y 90
> turn y -90
> turn x -90
> turn z -30
> turn z 60
> turn y 180
> select #9/O-S
2009 atoms, 2252 bonds, 95 pseudobonds, 98 residues, 2 models selected
> select ~sel & ##selected
64621 atoms, 65677 bonds, 97 pseudobonds, 8168 residues, 3 models selected
> hide sel cartoons
> set bgColor black
> set bgColor transparent
> hide #!9 models
> select clear
[Repeated 1 time(s)]
> select #3/3:160-169
74 atoms, 75 bonds, 10 residues, 1 model selected
> select #4/3:160-169
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #4/3:161-169
Nothing selected
> select #3/3:161-169
68 atoms, 69 bonds, 9 residues, 1 model selected
> turn y 10
> turn y -20
> turn y -5
[Repeated 1 time(s)]
> turn y 10
> turn y 15
> turn y -10
> set bgColor white
> set bgColor #ffffff00
> hide #!6 models
> hide #!5 models
> select add #3
2489 atoms, 2536 bonds, 315 residues, 2 models selected
> select subtract #3
6 models selected
> select add #3
2489 atoms, 2536 bonds, 315 residues, 1 model selected
> select add #4
7069 atoms, 7152 bonds, 615 residues, 8 models selected
> hide sel cartoons
> show sel surfaces
> color #3 #0096ffff
> color #4 #ffd479ff
> color #4 #ff9300ff
> color #4 #fffc79ff
> color #4 #73fcd6ff
> color #4 #73fa79ff
> color #4 #ff85ffff
> color #4 #ff8ad8ff
> color #4 #ff85ffff
> color #3 #00fa92ff
> color #3 #00f900ff
> color #3 #8efa00ff
> color #3 #fffb00ff
> color #3 #ff9300ff
> color #3 silver
> color #3 darkgrey
> color #3 silver
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!4 models
> show #!4 models
> color #2 #0096ffff
> color #3 #0096ffff
> color #3 silver
> color #3 #0096ffff
> color #3 silver
> color #4 #0096ffff
> select subtract #3
4580 atoms, 4616 bonds, 300 residues, 13 models selected
> select subtract #4
6 models selected
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
> own/ZF/ZFwhole_superimpose.tif" width 743 height 634 supersample 3
> transparentBackground true
> hide #!3 models
> show #!5 models
> hide #!5 models
> show #!3 models
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS
> own/ZF/ZFwhole_superimpose.tif" width 743 height 634 supersample 3
> transparentBackground true
> hide #!4 models
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/ZFwhole_DH.tif"
> width 743 height 634 supersample 3 transparentBackground true
> show #!4 models
> hide #!3 models
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/ZFwhole_sDH.tif"
> width 743 height 634 supersample 3 transparentBackground true
> save "/Users/fxy/OneDrive - connect.hku.hk/hSH_MS own/ZF/ZF_comparison.cxs"
> show #!9 models
> hide #!9 models
> show #!9 models
> select add #9
66630 atoms, 67929 bonds, 192 pseudobonds, 8266 residues, 4 models selected
> select add #10
187796 atoms, 190040 bonds, 201 pseudobonds, 16093 residues, 7 models selected
> show sel & #!9 cartoons
> hide #!4 models
> hide #!9 models
> show #!9 models
> show #!10 models
> hide sel surfaces
> cartoon style (#!9-10 & sel) modeHelix tube sides 20
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 1891, in
_update_graphics_if_needed
s[i].update_graphics_if_needed()
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 357, in update_graphics_if_needed
self._create_ribbon_graphics()
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 667, in _create_ribbon_graphics
ribbons_drawing.compute_ribbons(self)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 600, in compute_ribbons
_make_ribbon_graphics(structure, self)
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 141, in _make_ribbon_graphics
centers = _arc_helix_geometry(coords, xs_mgr, displays, start, end, geometry)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/ribbon.py", line 980, in _arc_helix_geometry
hc = HelixCylinder(coords[start:end])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 196, in __init__
self._straight_optimize()
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 409, in _straight_optimize
opt = OptLine(self.coords, centroid, axis)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/sse.py", line 36, in __init__
from scipy.optimize import minimize
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/__init__.py", line 409, in <module>
from ._optimize import *
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_optimize.py", line 38, in <module>
from ._numdiff import approx_derivative
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_numdiff.py", line 8, in <module>
from ._group_columns import group_dense, group_sparse
ImportError:
dlopen(/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so, 2): Symbol not
found:
__ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
Referenced from:
/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so (which was built
for Mac OS X 12.0)
Expected in: /usr/lib/libc++.1.dylib
Error processing trigger "graphics update":
ImportError:
dlopen(/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so, 2): Symbol not
found:
__ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
Referenced from:
/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_group_columns.cpython-311-darwin.so (which was built
for Mac OS X 12.0)
Expected in: /usr/lib/libc++.1.dylib
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/scipy/optimize/_numdiff.py", line 8, in
from ._group_columns import group_dense, group_sparse
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 71.0.7
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 6723.81.1
Software:
System Software Overview:
System Version: macOS 11.2.3 (20D91)
Kernel Version: Darwin 20.3.0
Time since boot: 3 days 5 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Duplicate of "won't fix" #15267