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Opened 3 years ago
Closed 3 years ago
#7781 closed defect (duplicate)
Session reset: 'Tasks' object has no attribute 'remove'
| Reported by: | Owned by: | Zach Pearson | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-12.0.1-arm64-arm-64bit
ChimeraX Version: 1.5.dev202208200154 (2022-08-20 01:54:23 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.5.dev202208200154 (2022-08-20)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> "/Users/sqx/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
> Support/com.tencent.xinWeChat/2.0b4.0.9/d59aab0e39bf10d09f81f42a27bd0ce4/Message/MessageTemp/8a83bcaec4de20f0a763aaf0de0734d6/File/20210520_SX180_refine_18.pdb"
Summary of feedback from opening
/Users/sqx/Library/Containers/com.tencent.xinWeChat/Data/Library/Application
Support/com.tencent.xinWeChat/2.0b4.0.9/d59aab0e39bf10d09f81f42a27bd0ce4/Message/MessageTemp/8a83bcaec4de20f0a763aaf0de0734d6/File/20210520_SX180_refine_18.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Date 2021-06-08 Time 13:39:21 CST +0800 (1623130761.80 s)
Ignored bad PDB record found on line 2
REMARK PHENIX refinement
Ignored bad PDB record found on line 4
REMARK ****************** INPUT FILES AND LABELS
******************************
Ignored bad PDB record found on line 5
REMARK Reflections:
Ignored bad PDB record found on line 6
REMARK file name :
/Users/guodonghe/Documents/Kobilka_Lab/Xtals/20210520_SX180/cc_3.02A_final/cluster_0382/run_03/Refine_1/20210520_SX180_refine_data.mtz
36 messages similar to the above omitted
Chain information for 20210520_SX180_refine_18.pdb #1
---
Chain | Description
A B | No description available
C G | No description available
D F | No description available
> show cartoons
> show atoms
> hide atoms
> set bgColor white
> set bgColor black
> set bgColor white
> set bgColor black
[Repeated 1 time(s)]
> set bgColor white
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)
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 5JQH
Summary of feedback from opening 5JQH fetched from pdb
---
notes | Fetching compressed mmCIF 5jqh from
http://files.rcsb.org/download/5jqh.cif
Fetching CCD CAU from http://ligand-expo.rcsb.org/reports/C/CAU/CAU.cif
5jqh title:
Structure of beta2 adrenoceptor bound to carazolol and inactive-state
stabilizing nanobody, Nb60 [more info...]
Chain information for 5jqh #2
---
Chain | Description | UniProt
A B | Endolysin,Beta-2 adrenergic receptor | ADRB2_HUMAN
C D | Nanobody60, Nb60 |
Non-standard residues in 5jqh #2
---
CAU — (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
((S)-Carazolol)
CLR — cholesterol
5jqh mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #!1 models
> color #2 bychain
> select #2/A:867-1343
2915 atoms, 2987 bonds, 2 pseudobonds, 391 residues, 2 models selected
> select #2/C:1-120
859 atoms, 875 bonds, 120 residues, 1 model selected
> select #2/B:866-1344
2989 atoms, 3059 bonds, 3 pseudobonds, 402 residues, 2 models selected
> select #2/D:1-117
838 atoms, 853 bonds, 117 residues, 1 model selected
> hide #2 /a
> hide #2 /a ribbons
> hide #2 /c ribbons
> show #!1 models
> hide #!2 models
> sym #2
5jqh mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chains A,C
2| author_and_software_defined_assembly| 1 copy of chains B,D
> log metadata #2
Metadata for 5jqh #2
---
Title | Structure of beta2 adrenoceptor bound to carazolol and inactive-state
stabilizing nanobody, Nb60
Citation | Staus, D.P., Strachan, R.T., Manglik, A., Pani, B., Kahsai, A.W.,
Kim, T.H., Wingler, L.M., Ahn, S., Chatterjee, A., Masoudi, A., Kruse, A.C.,
Pardon, E., Steyaert, J., Weis, W.I., Prosser, R.S., Kobilka, B.K., Costa, T.,
Lefkowitz, R.J. (2016). Allosteric nanobodies reveal the dynamic range and
diverse mechanisms of G-protein-coupled receptor activation. Nature, 535,
448-452. PMID: 27409812. DOI: 10.1038/nature18636
Non-standard residues | CAU —
(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol ((S)-Carazolol)
CLR — cholesterol
Gene sources | Homo sapiens (human)
Enterobacteria phage T4
Lama glama
Experimental method | X-ray diffraction
Resolution | 3.2Å
> log chains #2
Chain information for 5jqh #2
---
Chain | Description | UniProt
A B | Endolysin,Beta-2 adrenergic receptor | ADRB2_HUMAN
C D | Nanobody60, Nb60 |
> log metadata #1
No models had metadata
> log chains #1
Chain information for 20210520_SX180_refine_18.pdb #1
---
Chain | Description
A B | No description available
C G | No description available
D F | No description available
> select #1/A:29-342
2268 atoms, 2329 bonds, 1 pseudobond, 282 residues, 2 models selected
> select #1/A:29-342
2268 atoms, 2329 bonds, 1 pseudobond, 282 residues, 2 models selected
> select #1/B:29-342
2268 atoms, 2329 bonds, 1 pseudobond, 282 residues, 2 models selected
> select #1/G:1002-1161
1275 atoms, 1295 bonds, 160 residues, 1 model selected
> select #1/F:1-120
859 atoms, 875 bonds, 120 residues, 1 model selected
> select #1/B:29-342
2268 atoms, 2329 bonds, 1 pseudobond, 282 residues, 2 models selected
> select #1/G:1002-1161
1275 atoms, 1295 bonds, 160 residues, 1 model selected
> select #1/F:1-120
859 atoms, 875 bonds, 120 residues, 1 model selected
> hide #1 /b&g&h ribbons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 /b ribbons
> hide #1 /g ribbons
> hide #1 /h ribbons
> select #1/F:1-120
859 atoms, 875 bonds, 120 residues, 1 model selected
> hide #1 /f ribbons
> show #!2 models
> hide #!1 models
> ui mousemode right "rotate selected models"
[Repeated 1 time(s)]
> ui mousemode right select
> show #!1 models
> undo
[Repeated 2 time(s)]
> show #!2 models
> select #1/A:29-342
2268 atoms, 2329 bonds, 1 pseudobond, 282 residues, 2 models selected
> select #1/A:29-342
2268 atoms, 2329 bonds, 1 pseudobond, 282 residues, 2 models selected
> select #2/A:867-1343
2915 atoms, 2987 bonds, 2 pseudobonds, 391 residues, 2 models selected
> select #2/A:867-1343
2915 atoms, 2987 bonds, 2 pseudobonds, 391 residues, 2 models selected
> select #2/B:866-1344
2989 atoms, 3059 bonds, 3 pseudobonds, 402 residues, 2 models selected
> mmaker #1/a to #2/b
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 5jqh, chain B (#2) with 20210520_SX180_refine_18.pdb, chain A (#1),
sequence alignment score = 1461.2
RMSD between 277 pruned atom pairs is 0.488 angstroms; (across all 282 pairs:
1.282)
> select clear
[Repeated 1 time(s)]
> hide #!1 models
> show #!1 models
> select clear
> rename #2 b2+nb60
> rename #1 "from hgd"
> open 2RH1
Summary of feedback from opening 2RH1 fetched from pdb
---
notes | Fetching compressed mmCIF 2rh1 from
http://files.rcsb.org/download/2rh1.cif
Fetching CCD GLC from http://ligand-expo.rcsb.org/reports/G/GLC/GLC.cif
Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
Fetching CCD BU1 from http://ligand-expo.rcsb.org/reports/B/BU1/BU1.cif
Fetching CCD ACM from http://ligand-expo.rcsb.org/reports/A/ACM/ACM.cif
Fetching CCD PLM from http://ligand-expo.rcsb.org/reports/P/PLM/PLM.cif
Fetching CCD 12P from http://ligand-expo.rcsb.org/reports/1/12P/12P.cif
2rh1 title:
High resolution crystal structure of human B2-adrenergic G protein-coupled
receptor. [more info...]
Chain information for 2rh1 #3
---
Chain | Description | UniProt
A | beta-2-adrenergic receptor/T4-lysozyme chimera | ADRB2_HUMAN
Non-standard residues in 2rh1 #3
---
12P — dodecaethylene glycol (polyethylene glycol PEG400)
ACM — acetamide
BU1 — 1,4-butanediol
CAU — (2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol
((S)-Carazolol)
CLR — cholesterol
GLC — alpha-D-glucopyranose (alpha-D-glucose; D-glucose; glucose)
PLM — palmitic acid
SO4 — sulfate ion
> hide #!1 models
> hide #!2 models
> hide #3 atoms
> color #3 bychain
> rename #3 b2+T4L
> show #!2 models
> show #!1 models
> hide #!1 models
> select #2/A:867-1343
2915 atoms, 2987 bonds, 2 pseudobonds, 391 residues, 2 models selected
> select #2/B:866-1344
2989 atoms, 3059 bonds, 3 pseudobonds, 402 residues, 2 models selected
> mmaker #3/A to #2/b
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker b2+nb60, chain B (#2) with b2+T4L, chain A (#3), sequence alignment
score = 1313.2
RMSD between 274 pruned atom pairs is 0.459 angstroms; (across all 284 pairs:
2.189)
> select clear
> show #!1 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #3 models
> open 6CM¥
'6CM¥' has no suffix
> open 6CM¥
'6CM¥' has no suffix
> open 6CM4
Summary of feedback from opening 6CM4 fetched from pdb
---
notes | Fetching compressed mmCIF 6cm4 from
http://files.rcsb.org/download/6cm4.cif
Fetching CCD 8NU from http://ligand-expo.rcsb.org/reports/8/8NU/8NU.cif
Fetching CCD PEG from http://ligand-expo.rcsb.org/reports/P/PEG/PEG.cif
Fetching CCD OLA from http://ligand-expo.rcsb.org/reports/O/OLA/OLA.cif
6cm4 title:
Structure of the D2 Dopamine Receptor Bound to the Atypical Antipsychotic Drug
Risperidone [more info...]
Chain information for 6cm4 #4
---
Chain | Description | UniProt
A | D(2) dopamine receptor, endolysin chimera | DRD2_HUMAN
Non-standard residues in 6cm4 #4
---
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
OLA — oleic acid
PEG — di(hydroxyethyl)ether
> open 6CM4
6cm4 title:
Structure of the D2 Dopamine Receptor Bound to the Atypical Antipsychotic Drug
Risperidone [more info...]
Chain information for 6cm4 #5
---
Chain | Description | UniProt
A | D(2) dopamine receptor, endolysin chimera | DRD2_HUMAN
Non-standard residues in 6cm4 #5
---
8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
OLA — oleic acid
PEG — di(hydroxyethyl)ether
> hide #!1 models
> hide #!2 models
> hide #!4 models
> ui tool show "Side View"
> view
> show #!4 models
> show #3 models
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> hide #3 models
> hide #!4 models
> hide #!5 atoms
> color #!5 bychain
> color #5 hot pink
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color dark turquoise
> color dark salmon
> color salmon
> color light salmon
> undo
[Repeated 3 time(s)]
> color #5 orange red
> color #5 cornflower blue
> close #4
> rename #5 D2+T4L
> mmaker #5 to #2/b
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker b2+nb60, chain B (#2) with D2+T4L, chain A (#5), sequence alignment
score = 751.1
RMSD between 7 pruned atom pairs is 1.268 angstroms; (across all 184 pairs:
21.135)
> show #!2 models
> mmaker #5 to #1/b
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker from hgd, chain B (#1) with D2+T4L, chain A (#5), sequence
alignment score = 524.3
RMSD between 166 pruned atom pairs is 1.017 angstroms; (across all 258 pairs:
5.241)
> show #!1 models
> show #3 models
> mmaker #5 to #1/a
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker from hgd, chain A (#1) with D2+T4L, chain A (#5), sequence
alignment score = 520.9
RMSD between 167 pruned atom pairs is 1.044 angstroms; (across all 256 pairs:
5.306)
> hide #!2 models
> hide #3 models
Alignment identifier is 1
Alignment identifier is 2
Alignment identifier is 3
Alignment identifier is 4
Alignment identifier is 5
Alignment identifier is 3/A
Alignment identifier is 5/A
Alignment identifier is 6
Alignment identifier is 7
Alignment identifier is 8
Alignment identifier is 9
Alignment identifier is 10
Destroying pre-existing alignment with identifier 3/A
Alignment identifier is 3/A
Destroying pre-existing alignment with identifier 5/A
Alignment identifier is 5/A
> ui tool show "Modeller Comparative"
> help help:user/tools/modeller.html
> rename #1 b2+T4L+nb60
> show #!2 models
> show #3 models
> hide #!2 models
> hide #3 models
> select clear
[Repeated 1 time(s)]
> show #!1 target m
> log metadata #1
No models had metadata
> log chains #1
Chain information for b2+T4L+nb60 #1
---
Chain | Description
A B | No description available
C G | No description available
D F | No description available
> select #1/B:29-342
2268 atoms, 2329 bonds, 1 pseudobond, 282 residues, 2 models selected
> select #1/A:29-342
2268 atoms, 2329 bonds, 1 pseudobond, 282 residues, 2 models selected
> hide #!1 models
> show #!2 models
> hide #!5 models
> hide #!2 atoms
> show #!5 models
> sym #2
b2+nb60 mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chains A,C
2| author_and_software_defined_assembly| 1 copy of chains B,D
> log metadata #2
Metadata for b2+nb60 #2
---
Title | Structure of beta2 adrenoceptor bound to carazolol and inactive-state
stabilizing nanobody, Nb60
Citation | Staus, D.P., Strachan, R.T., Manglik, A., Pani, B., Kahsai, A.W.,
Kim, T.H., Wingler, L.M., Ahn, S., Chatterjee, A., Masoudi, A., Kruse, A.C.,
Pardon, E., Steyaert, J., Weis, W.I., Prosser, R.S., Kobilka, B.K., Costa, T.,
Lefkowitz, R.J. (2016). Allosteric nanobodies reveal the dynamic range and
diverse mechanisms of G-protein-coupled receptor activation. Nature, 535,
448-452. PMID: 27409812. DOI: 10.1038/nature18636
Non-standard residues | CAU —
(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol ((S)-Carazolol)
CLR — cholesterol
Gene sources | Homo sapiens (human)
Enterobacteria phage T4
Lama glama
Experimental method | X-ray diffraction
Resolution | 3.2Å
> log chains #2
Chain information for b2+nb60 #2
---
Chain | Description | UniProt
A B | Endolysin,Beta-2 adrenergic receptor | ADRB2_HUMAN
C D | Nanobody60, Nb60 |
> select #2/B:866-1344
2989 atoms, 3059 bonds, 3 pseudobonds, 402 residues, 2 models selected
> select #2/B:866-1344
2989 atoms, 3059 bonds, 3 pseudobonds, 402 residues, 2 models selected
> select #2/A:867-1343
2915 atoms, 2987 bonds, 2 pseudobonds, 391 residues, 2 models selected
> select #2/B:866-1344
2989 atoms, 3059 bonds, 3 pseudobonds, 402 residues, 2 models selected
> sequence chain #2/b
Alignment identifier is 2/B
> sequence chain #5
Alignment identifier is 5/A
> select clear
Drag select of 31 residues
> select clear
> select #5/A:69
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:151
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:1153
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!5 models
> select #2/B:1129
7 atoms, 6 bonds, 1 residue, 1 model selected
> select
> #2/B:868-874,924-946,949-954,957-971,974-988,990-998,1001-1021,1023-1096,1101-1136,1146-1171,1178-1187,1196-1229,1262-1299,1304-1319,1321-1327,1329-1340
2598 atoms, 2643 bonds, 349 residues, 1 model selected
> select clear
> select #2/B:1127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1130
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1130-1133
42 atoms, 43 bonds, 4 residues, 1 model selected
> select #2/B:1131
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:1131
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right label
> label delete residues
> label #2/B:1131
[Repeated 1 time(s)]
> label sel attribute name
> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"
> label sel text "R 3.50"
> label height 0.1
> undo
> style sel stick
Changed 11 atom styles
> show sel atoms
> style sel stick
Changed 11 atom styles
> label height 1
> color sel byhetero
> show #!5 models
> select #5/A:131
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:132
11 atoms, 10 bonds, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00a0' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon ' ' for virtual key 49 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> show sel atoms
> color sel byhetero
> ui mousemode right "move label"
> select clear
> hide #!5 models
> select #2/B:1270
5 atoms, 4 bonds, 1 residue, 1 model selected
> select
> #2/B:868-874,924-946,949-954,957-971,974-988,990-998,1001-1021,1023-1096,1101-1136,1146-1171,1178-1187,1196-1229,1262-1299,1304-1319,1321-1327,1329-1340
2598 atoms, 2643 bonds, 349 residues, 1 model selected
> select clear、
Expected an objects specifier or a keyword
> select clear
> select #2/B:1268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:1268-1269
19 atoms, 19 bonds, 2 residues, 1 model selected
> select #2/B:1268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:1268
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> ui mousemode right distance
> ui mousemode right label
> label #2/B:1268
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 '\u5e2e' 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 '\u5e2e' 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)
> label sel text "E 6.30"
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> label height 1
> show #!5 models
> select #5/A:369
5 atoms, 4 bonds, 1 residue, 1 model selected
> select
> #5/A:35-98,103-138,146-176,182-186,188-196,198-222,368-399,404-418,421-441,1002-1011,1038-1051,1059-1081,1084-1112,1114-1123,1125-1134,1136-1156
2668 atoms, 2710 bonds, 355 residues, 1 model selected
> select clear
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:368-369
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> style sel stick
Changed 9 atom styles
> show sel atoms
> hide #!2 models
> color sel byhetero
> select #5/A:377
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:122
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:121-125
35 atoms, 34 bonds, 5 residues, 1 model selected
> select #5/A:120
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:120-125
40 atoms, 39 bonds, 6 residues, 1 model selected
> select clear
> select #5/A:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:121
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:121,125
14 atoms, 12 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel red
> color sel cornflower blue
> color sel light sea green
> color sel byhetero
> label delete residues
> show #!2 models
> hide #!5 models
> hide #!2 models
> show #!5 models
> show #!2 models
> ui mousemode right distance
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
Drag select of 4 residues
> select clear
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:132
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:132
11 atoms, 10 bonds, 1 residue, 1 model selected
> select
> #5/A:35-98,103-138,146-176,182-186,188-196,198-222,368-399,404-418,421-441,1002-1011,1038-1051,1059-1081,1084-1112,1114-1123,1125-1134,1136-1156
2668 atoms, 2710 bonds, 355 residues, 1 model selected
> select clear
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> select
> #5/A:35-98,103-138,146-176,182-186,188-196,198-222,368-399,404-418,421-441,1002-1011,1038-1051,1059-1081,1084-1112,1114-1123,1125-1134,1136-1156
2668 atoms, 2710 bonds, 355 residues, 1 model selected
> select clear
> select #2/B:1132
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:132
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:129
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:129-138
77 atoms, 77 bonds, 10 residues, 1 model selected
> ui tool show "Modeller Comparative"
> modeller comparative 2/B:1 5/A:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
No Modeller license key provided. Get a license key by registering at the
Modeller web site.
> modeller comparative 2/B:1 5/A:1 numModels 5 fast false multichain true
> hetPreserve false hydrogens false waterPreserve false
Webservices job id: G5D6F4RLCNHL8BF3
> show sel atoms
> undo
> show #3 models
> hide #3 models
> select add #5
3236 atoms, 3286 bonds, 2 pseudobonds, 446 residues, 2 models selected
> show sel atoms
[Repeated 1 time(s)]
> select add #2
10937 atoms, 11170 bonds, 7 pseudobonds, 1480 residues, 4 models selected
> show sel atoms
> select subtract #2
3236 atoms, 3286 bonds, 2 pseudobonds, 446 residues, 2 models selected
> select subtract #5
Nothing selected
> undo
[Repeated 2 time(s)]Modeller job ID G5D6F4RLCNHL8BF3 finished
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 D2+T4L, chain A (#5) with target, chain A (#), sequence alignment
score = 2186.6
RMSD between 423 pruned atom pairs is 0.420 angstroms; (across all 423 pairs:
0.420)
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 D2+T4L, chain A (#5) with target, chain A (#), sequence alignment
score = 2194.4
RMSD between 329 pruned atom pairs is 0.636 angstroms; (across all 423 pairs:
1.615)
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 D2+T4L, chain A (#5) with target, chain A (#), sequence alignment
score = 2186.6
RMSD between 423 pruned atom pairs is 0.299 angstroms; (across all 423 pairs:
0.299)
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 D2+T4L, chain A (#5) with target, chain A (#), sequence alignment
score = 2206.4
RMSD between 253 pruned atom pairs is 0.378 angstroms; (across all 423 pairs:
3.415)
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 D2+T4L, chain A (#5) with target, chain A (#), sequence alignment
score = 2183.6
RMSD between 325 pruned atom pairs is 0.625 angstroms; (across all 423 pairs:
1.796)
Associated target chain A to chain B with 236 mismatches and/or gaps
[Repeated 4 time(s)]Associated target chain A to chain A with 0 mismatches
[Repeated 4 time(s)] Chain information for target
---
Chain | Description
4.1/A 4.2/A 4.3/A 4.4/A 4.5/A | No description available
> select clear
> hide #!4 models
> hide #!2 models
> hide #!5 models
> hide #4.1 models
> show #!4 models
> show #4.1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> ui tool show "Modeller Comparative"
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> show #3 models
> hide #3 models
> show #!2 models
> hide #!2 models
> show #!5 models
> hide #!5 models
> hide #!4 models
> hide #4.1 models
> hide #4.2 models
> hide #4.3 models
> hide #4.4 models
> hide #4.5 models
> show #!5 models
> show #3 models
> hide #3 models
> show #3 models
> select #3/A:131
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #3/A:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> undo
> show #!2 models
> hide #3 models
> show #3 models
> hide #!2 models
> select #3/A:268
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!2 models
> hide #!5 models
> select #4.1/A:174-187,198-243,294 #4.2/A:174-187,198-243,294
> #4.3/A:174-187,198-243,294 #4.4/A:174-187,198-243,294
> #4.5/A:174-187,198-243,294 #2/B:1027-1261,1343-1344
4025 atoms, 4086 bonds, 1 pseudobond, 512 residues, 7 models selected
> select
> #2/B:866-875,924-946,949-955,957-988,990-1021,1023-1096,1101-1136,1146-1171,1178-1187,1196-1229,1262-1299,1304-1340
> #4.1/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
> #4.2/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
> #4.3/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
> #4.4/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
> #4.5/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
11214 atoms, 11407 bonds, 1 pseudobond, 1403 residues, 7 models selected
> select clear
> select
> #2/B:866-875,924-946,949-955,957-988,990-1021,1023-1096,1101-1136,1146-1171,1178-1187,1196-1229,1262-1299,1304-1340
> #4.1/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
> #4.2/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
> #4.3/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
> #4.4/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
> #4.5/A:174-197,226-237,246-268,271-277,279-310,312-343,345-386,391-413,415-428
11214 atoms, 11407 bonds, 1 pseudobond, 1403 residues, 7 models selected
> select clear
> select
> #5/A:35-98,103-138,145-176,182-222,367-399,404-441,1002-1011,1038-1051,1059-1081,1084-1123,1125-1156
> #4.1/A:1-64,69-104,111-142,148-198,225-238,246-268,271-310,312-343,354-386,391-428
> #4.2/A:1-64,69-104,111-142,148-198,225-238,246-268,271-310,312-343,354-386,391-428
> #4.3/A:1-64,69-104,111-142,148-198,225-238,246-268,271-310,312-343,354-386,391-428
> #4.4/A:1-64,69-104,111-142,148-198,225-238,246-268,271-310,312-343,354-386,391-428
> #4.5/A:1-64,69-104,111-142,148-198,225-238,246-268,271-310,312-343,354-386,391-428
17146 atoms, 17444 bonds, 2178 residues, 6 models selected
> hide #3 models
> show #!5 models
> select clear
> hide #!5 models
> show #!2 atoms
> sym #2
b2+nb60 mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chains A,C
2| author_and_software_defined_assembly| 1 copy of chains B,D
> log metadata #2
Metadata for b2+nb60 #2
---
Title | Structure of beta2 adrenoceptor bound to carazolol and inactive-state
stabilizing nanobody, Nb60
Citation | Staus, D.P., Strachan, R.T., Manglik, A., Pani, B., Kahsai, A.W.,
Kim, T.H., Wingler, L.M., Ahn, S., Chatterjee, A., Masoudi, A., Kruse, A.C.,
Pardon, E., Steyaert, J., Weis, W.I., Prosser, R.S., Kobilka, B.K., Costa, T.,
Lefkowitz, R.J. (2016). Allosteric nanobodies reveal the dynamic range and
diverse mechanisms of G-protein-coupled receptor activation. Nature, 535,
448-452. PMID: 27409812. DOI: 10.1038/nature18636
Non-standard residues | CAU —
(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol ((S)-Carazolol)
CLR — cholesterol
Gene sources | Homo sapiens (human)
Enterobacteria phage T4
Lama glama
Experimental method | X-ray diffraction
Resolution | 3.2Å
> log chains #2
Chain information for b2+nb60 #2
---
Chain | Description | UniProt
A B | Endolysin,Beta-2 adrenergic receptor | ADRB2_HUMAN
C D | Nanobody60, Nb60 |
> select #2/D:1-117
838 atoms, 853 bonds, 117 residues, 1 model selected
> sequence chain #2/d
Alignment identifier is 2/D
> select add #2
7701 atoms, 7884 bonds, 5 pseudobonds, 1034 residues, 2 models selected
> select subtract #2
Nothing selected
> select #2/D:102
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/D:102-103
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/D:106
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/D:106
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/D:102-103,106
30 atoms, 30 bonds, 3 residues, 1 model selected
> color sel byhetero
> ui mousemode right label
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select clear
> hide #2 /a atoms
> hide #2 /c atoms
> select #2/b & /d zr<5
Expected a keyword
> select #2/b & /d zr<5
Expected a keyword
> select : .b & :.d zr<5
Expected an objects specifier or a keyword
> interfaces #2/b & #2/d
No atoms specified
> select zone #2/b.d 5
Missing or invalid "near" argument: only initial part "#2/b" of atom specifier
valid
> select zone #2/b
Missing or invalid "range" argument: Expected a number
> select zone 2
Missing or invalid "near" argument: invalid objects specifier
> select zone #2/d 5 #2/b residues true
Selected 230 atoms
> hide sel atoms
[Repeated 2 time(s)]
> select add #2
7701 atoms, 7884 bonds, 5 pseudobonds, 1034 residues, 3 models selected
> hide sel atoms
> select zone #2/d 5 #2/b residues true
Selected 230 atoms
> hide sel atoms
> select add #2
7701 atoms, 7884 bonds, 5 pseudobonds, 1034 residues, 3 models selected
> hide sel atoms
> select zone #2/d 5 #2/b residues true
Selected 230 atoms
> show sel atoms
> color sel byhetero
> select
41068 atoms, 41935 bonds, 9 pseudobonds, 5271 residues, 14 models selected
> select clear
> show #!5 models
> hide #!2,5 atoms
> undo
> select add #5
3236 atoms, 3286 bonds, 2 pseudobonds, 446 residues, 2 models selected
> hide sel atoms
> select subtract #5
Nothing selected
> select #2/B:1268
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> hide #!5 models
> select #2/B:1131
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel red
> color sel byhetero
> select #2/B:1268
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> ui mousemode right label
> label #2/B:1268
> label sel text E6.30
> label #2/B:1131
> label sel text R3.50
> undo
> label sel text E6.30
> select #2/B:1131
11 atoms, 10 bonds, 1 residue, 1 model selected
> label #2/B:1131
> label sel text "R 3.50"
> label sel text R3.50
> show #!5 models
> hide #!5 models
> select zone #2/b 5#2/d res t
Missing or invalid "range" argument: Expected a number
> select zone #2/b 5 #2/d residues true
Selected 122 atoms
> show sel atoms
> select clear
> toolshed show
> ui tool show H-Bonds
> show #3 models
> hide #3 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/A:369
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
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)
> show sel atoms
> select #5/A:132
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right label
> ui mousemode right distance
[Repeated 1 time(s)]
> select clear
> ui mousemode right distance
> distance #5/A:368@OE1 #2/B:1131@NH2
Distance between D2+T4L #5/A GLU 368 OE1 and b2+nb60 #2/B ARG 1131 NH2: 3.956Å
> distance #2/B:1268@OE1 #5/A:132@NH2
Distance between b2+nb60 #2/B GLU 1268 OE1 and D2+T4L #5/A ARG 132 NH2: 6.416Å
> hide #!5 models
> show #!5 models
> ~distance #2/B:1268@OE1 #5/A:132@NH2
> ~distance #5/A:368@OE1 #2/B:1131@NH2
> distance #5/A:368@OE1 #5/A:132@NH2
Distance between D2+T4L #5/A GLU 368 OE1 and ARG 132 NH2: 3.612Å
> distance #2/B:1268@OE1 #2/B:1131@NH2
Distance between b2+nb60 #2/B GLU 1268 OE1 and ARG 1131 NH2: 6.998Å
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> ui tool show H-Bonds
> hbonds sel reveal true log true
Atom specifier selects no atoms
> show #!5 models
> hide #!5 models
> select zone #2/b 5 #2/d residues true
Selected 122 atoms
> name sel b
"sel" is reserved and cannot be redefined
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)
> name nb60-inter sel
> select zone #2/d 5 #2/b residues true
Selected 230 atoms
> name b2-inter sel
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select clear
> select b2-inter
Nothing selected
> select nb60-inter
Nothing selected
> select b2-inter residues true
Nothing selected
> select
41068 atoms, 41935 bonds, 11 pseudobonds, 5271 residues, 16 models selected
> select clear
> select b2-inter
Nothing selected
> select #2/D:103
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 b2+T4L+nb60
2 b2+nb60
3 b2+T4L
5 D2+T4L
4.1 target
4.2 target
4.3 target
4.4 target
4.5 target
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
b2+T4L+nb60 #1/A ASN 69 ND2 b2+nb60 #2/D PHE 103 O no hydrogen 2.884 N/A
b2+nb60 #2/B ASN 1069 ND2 b2+nb60 #2/D PHE 103 O no hydrogen 2.887 N/A
b2+T4L #3/A ASN 69 ND2 b2+nb60 #2/D PHE 103 O no hydrogen 2.500 N/A
3 hydrogen bonds found
> show #!1 models
> hide #!1 models
> cartoon suppressBackboneDisplay false
> ui tool show H-Bonds
> hide solvent
> select #2/D:104
6 atoms, 5 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 b2+T4L+nb60
2 b2+nb60
3 b2+T4L
5 D2+T4L
4.1 target
4.2 target
4.3 target
4.4 target
4.5 target
7 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
b2+T4L+nb60 #1/D GLY 101 N b2+nb60 #2/D SER 104 O no hydrogen 3.331 N/A
b2+nb60 #2/D GLY 101 N b2+nb60 #2/D SER 104 O no hydrogen 2.864 N/A
b2+nb60 #2/D SER 104 OG b2+T4L+nb60 #1/A ARG 63 O no hydrogen 3.269 N/A
b2+nb60 #2/D SER 104 OG b2+nb60 #2/B ARG 1063 O no hydrogen 3.162 N/A
b2+nb60 #2/D SER 104 OG b2+nb60 #2/D ILE 105 O no hydrogen 3.510 N/A
b2+nb60 #2/D SER 104 OG b2+T4L #3/A ARG 63 O no hydrogen 3.283 N/A
b2+T4L #3/A ARG 63 NE b2+nb60 #2/D SER 104 OG no hydrogen 3.031 N/A
7 hydrogen bonds found
> select #2/B:1063
11 atoms, 10 bonds, 1 residue, 1 model selected
> select clear
> show #!5 models
> hide #7 models
> log metadata #5
Metadata for D2+T4L #5
---
Title | Structure of the D2 Dopamine Receptor Bound to the Atypical
Antipsychotic Drug Risperidone
Citation | Wang, S., Che, T., Levit, A., Shoichet, B.K., Wacker, D., Roth,
B.L. (2018). Structure of the D2 dopamine receptor bound to the atypical
antipsychotic drug risperidone. Nature, 555, 269-273. PMID: 29466326. DOI:
10.1038/nature25758
Non-standard residues | 8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
OLA — oleic acid
PEG — di(hydroxyethyl)ether
Gene sources | Homo sapiens (human)
Enterobacteria phage T4 (bacteriophage t4)
Experimental method | X-ray diffraction
Resolution | 2.867Å
> log chains #5
Chain information for D2+T4L #5
---
Chain | Description | UniProt
A | D(2) dopamine receptor, endolysin chimera | DRD2_HUMAN
> log metadata #5
Metadata for D2+T4L #5
---
Title | Structure of the D2 Dopamine Receptor Bound to the Atypical
Antipsychotic Drug Risperidone
Citation | Wang, S., Che, T., Levit, A., Shoichet, B.K., Wacker, D., Roth,
B.L. (2018). Structure of the D2 dopamine receptor bound to the atypical
antipsychotic drug risperidone. Nature, 555, 269-273. PMID: 29466326. DOI:
10.1038/nature25758
Non-standard residues | 8NU —
3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one
OLA — oleic acid
PEG — di(hydroxyethyl)ether
Gene sources | Homo sapiens (human)
Enterobacteria phage T4 (bacteriophage t4)
Experimental method | X-ray diffraction
Resolution | 2.867Å
> log chains #5
Chain information for D2+T4L #5
---
Chain | Description | UniProt
A | D(2) dopamine receptor, endolysin chimera | DRD2_HUMAN
> select #5/A:35-442
1948 atoms, 1995 bonds, 2 pseudobonds, 263 residues, 3 models selected
> select #5/A:35-442
1948 atoms, 1995 bonds, 2 pseudobonds, 263 residues, 3 models selected
> select clear
> select zone #5/a 5 #2/d residues true
Selected 136 atoms
> select zone #2/d 5 #5/a residues true
Selected 201 atoms
> show sel atoms
> color sel byhetero
> select clear
> show hbonds
> hide #!5 models
> show #7 models
> show #!5 models
> sym #2
b2+nb60 mmCIF Assemblies
---
1| author_and_software_defined_assembly| 1 copy of chains A,C
2| author_and_software_defined_assembly| 1 copy of chains B,D
> log metadata #2
Metadata for b2+nb60 #2
---
Title | Structure of beta2 adrenoceptor bound to carazolol and inactive-state
stabilizing nanobody, Nb60
Citation | Staus, D.P., Strachan, R.T., Manglik, A., Pani, B., Kahsai, A.W.,
Kim, T.H., Wingler, L.M., Ahn, S., Chatterjee, A., Masoudi, A., Kruse, A.C.,
Pardon, E., Steyaert, J., Weis, W.I., Prosser, R.S., Kobilka, B.K., Costa, T.,
Lefkowitz, R.J. (2016). Allosteric nanobodies reveal the dynamic range and
diverse mechanisms of G-protein-coupled receptor activation. Nature, 535,
448-452. PMID: 27409812. DOI: 10.1038/nature18636
Non-standard residues | CAU —
(2S)-1-(9H-Carbazol-4-yloxy)-3-(isopropylamino)propan-2-ol ((S)-Carazolol)
CLR — cholesterol
Gene sources | Homo sapiens (human)
Enterobacteria phage T4
Lama glama
Experimental method | X-ray diffraction
Resolution | 3.2Å
> log chains #2
Chain information for b2+nb60 #2
---
Chain | Description | UniProt
A B | Endolysin,Beta-2 adrenergic receptor | ADRB2_HUMAN
C D | Nanobody60, Nb60 |
> select #2/D:1-117
838 atoms, 853 bonds, 2 pseudobonds, 117 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel atoms
> hide sel atoms
> hide #!5 models
> select #2/B:1275
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #7 models
> show #!5 models
> select #5/A:375
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1274
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:1274
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:375
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1274
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:374@SD
1 atom, 1 residue, 1 model selected
> select #2/B:1271
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #!5 models
> select #2/B:1274
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:1272
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1267
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:1264
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:1332
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:1329
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:1331
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1141
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/B:1142
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:1143
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:1144@CA
1 atom, 1 residue, 1 model selected
> select #2/B:1145
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1146
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:1062
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1063
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:1065
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> select #2/B:1066
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:1069
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1072
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1069
8 atoms, 7 bonds, 1 residue, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> show #!5 models
> select #5/A:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:69
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!5 models
> select #2/B:1068
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!5 models
> select #5/A:67
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:69
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:64
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:63
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:64
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:63
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1063@CB
1 atom, 1 residue, 1 model selected
> select #2/B:1062
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:148
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #2/d ribbons
> select #5/A:68
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> toolshed show
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)
> align #2/b toAtoms #5/a
Unequal number of atoms to pair, 3039 and 3236
> align #2/b toAtoms #5/a move residues each chain
Unequal number of atoms to pair, 3039 and 3236
> close #4
> ui mousemode right zoom
> select #2/B:1034
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:1033
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:35
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1033
7 atoms, 6 bonds, 1 residue, 1 model selected
> align #2/b:1033-1340 toAtoms #5/a:35-441 move residues each chain
Unequal number of atoms to pair, 2148 and 1943
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)
> mmaker #5/a to #2/b 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 b2+nb60, chain B (#2) with D2+T4L, chain A (#5), sequence alignment
score = 751.1
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: b2+nb60 #2/B, D2+T4L #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 7 pruned atom pairs is 1.268 angstroms; (across all 184 pairs:
21.135)
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)
> show #3 models
> hide #!2 models
> mmaker #5 to #3 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 b2+T4L, chain A (#3) with D2+T4L, chain A (#5), sequence alignment
score = 1497.2
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: b2+T4L #3/A, D2+T4L #5/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 166 pruned atom pairs is 1.003 angstroms; (across all 416 pairs:
16.765)
> show #!2 models
> hide #3 models
> select #5/A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:72
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #3/A:39-61,64-87,89-97,108-132,134-137,146-147,150-151,153-165,201,204-216,218-219,222,274-290,310-327,329-340
> #5/A:40-62,65-88,90-98,109-133,135-138,148-149,152-153,155-167,191,194-206,208-209,212,374-390,410-427,430-441
2543 atoms, 2573 bonds, 332 residues, 2 models selected
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #5/A:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!2 models
> select #5/A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:138@CA
1 atom, 1 residue, 1 model selected
> select #5/A:139
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:144@CA
1 atom, 1 residue, 1 model selected
> show #3 models
> show #!2 models
> hide #!2 models
> hide #3 models
> show #!2 models
> show #3 models
> select #2/B:1145@CA
1 atom, 1 residue, 1 model selected
> hide #!2 models
> select #3/A:145
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #3/A:147
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:148
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:146
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:144
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:146
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:144
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:145
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:146
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
> select #5/A:144
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:147
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:148
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #!2 models
> select #2/B:1146
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!2 models
> select #5/A:375
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> select #2/B:1275
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!5 models
> hide #!2 models
> select #5/A:375
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:374
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:372
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:371
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:370
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #!2 models
> select #2/B:1271
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:371
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:370
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:270
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:370
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #!2 models
> select #3/A:223
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:367
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:365
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:364
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #!2 models
> select #5/A:367
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1267
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:367
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1265
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1264
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #5/A:365
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:364
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #!2 models
> select #5/A:430@CB
1 atom, 1 residue, 1 model selected
> select #5/A:433
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!6 models
> hide #!5 models
> hide #3 models
> show #3 models
> show #!5 models
> hide #3 models
> hide #!5 models
> select zone #2/b 5 #2/d residues true
Selected 122 atoms
> show
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select #2/B:1332
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #!5 models
> hide #!5 models
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)
> ui mousemode right label
> label #2/B:1332
> label #2 text F8.50
> undo
[Repeated 1 time(s)]
> ~label sel residues
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)
> clear labels
Unknown command: clear labels
> clear label
Unknown command: clear label
> hide lable
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> label delete
> label delete #2
> select #2/D:103
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/D:102-103
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/D:102-103
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #2/D:102-103,106
30 atoms, 30 bonds, 3 residues, 1 model selected
> label sel
> select clear
> select #2/B:1268
9 atoms, 8 bonds, 1 residue, 1 model selected
> lable sel E6.30
Unknown command: lable sel E6.30
> lable sel text E6.30
Unknown command: lable sel text E6.30
> label #2/B:1268
> label sel text E6.30
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #2/B:1332@CD1
1 atom, 1 residue, 1 model selected
> select #2/B:1332
11 atoms, 11 bonds, 1 residue, 1 model selected
> lable sel text F8.50
Unknown command: lable sel text F8.50
> label sel text F8.50
> ui mousemode right "move label"
> select #5/A:73
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 1 residues
> select #2/B:1072
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:73@CG1
1 atom, 1 residue, 1 model selected
> select #2/B:1069
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:70
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!5 models
> select #2/B:1069
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right label
> label #2/B:1069
> label sel text N2.40
> ui mousemode right "move label"
> color sel orange
> color sel byhetero
> select #2/B:1267@CD
1 atom, 1 residue, 1 model selected
> select #2/B:1332
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel orange
> show #7 models
> select #2/B:1329
6 atoms, 5 bonds, 1 residue, 1 model selected
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #3 models
> hide #3 models
> show #!5 models
> ui mousemode right label
> label #2/B:1329
> lable sel text S8.47
Unknown command: lable sel text S8.47
> label sel text S8.47
> color sel orange
> color sel byhetero
> select #2/B:1274
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/B:1269
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:374
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1274
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel orange
> select #5/A:374
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1274
7 atoms, 6 bonds, 1 residue, 1 model selected
> label sel text T6.36
> color sel byhetero
> select #5/A:374
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel lightblue purple
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> ui tool show "Color Actions"
> color sel medium purple
> color sel medium orchid
> color sel dark violet
> color sel deep pink
> color sel dark violet
> color sel hot pink
> color sel orchid
> color sel medium orchid
> color sel plum
> color sel violet
> color sel light pink
> color sel khaki
> color sel pale goldenrod
> color sel plum
> color sel byhetero
> select #5/A:430
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> color sel byhetero
> select #5/A:64
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1063
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/D:104
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:64
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1063
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel orange
> color sel byhetero
> label sel text R12.49
> ui mousemode right "move label"
> select #5/A:64
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #5/A:432
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #!2 models
> select #2/B:1331
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> select #5/A:370
5 atoms, 4 bonds, 1 residue, 1 model selected
> show #!2 models
> select #2/B:1267
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:370
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:374
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #2/B:1275@CA
1 atom, 1 residue, 1 model selected
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:1267
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:367@CA
1 atom, 1 residue, 1 model selected
> select #2/B:1264
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:1267
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:1264
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:1141@CD2
1 atom, 1 residue, 1 model selected
> select #5/A:367
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1267
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel orange
> color sel byhetero
> label sel text K6.29
> hide #!5 models
> hide #7 models
> show #7 models
> hide #7 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> ui tool show Contacts
> select #2/D:106
12 atoms, 12 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 4.9999999999999964 ignoreHiddenModels true log
> true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
124 distances
atom1 atom2 distance
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B GLU 1268 OE2 2.711
b2+nb60 #2/D TYR 106 N b2+nb60 #2/D VAL 99 O 2.863
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D VAL 99 N 3.076
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B LYS 1267 CD 3.262
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D ALA 97 O 3.319
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B LYS 1267 CE 3.353
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D VAL 99 O 3.373
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B GLU 1268 CD 3.518
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D LYS 98 CA 3.612
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B GLU 1268 OE2 3.651
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B LYS 1267 NZ 3.658
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/B GLU 1268 OE1 3.678
b2+nb60 #2/D TYR 106 CA b2+nb60 #2/D VAL 99 O 3.706
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D TYR 108 N 3.726
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/D SER 104 O 3.741
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D LYS 98 C 3.744
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/B GLU 1268 OE2 3.749
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B LYS 1267 CG 3.764
b2+nb60 #2/D TYR 106 CB b2+nb60 #2/D TYR 108 CE2 3.777
b2+nb60 #2/D TYR 106 CB b2+nb60 #2/D VAL 99 O 3.828
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/D SER 104 O 3.835
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D TYR 108 CD2 3.862
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/B GLU 1268 CD 3.873
b2+nb60 #2/D TYR 106 N b2+nb60 #2/D SER 104 O 3.918
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/D ILE 105 C 3.953
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D VAL 99 CA 3.959
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D VAL 99 O 3.977
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D ILE 105 CG2 3.980
b2+nb60 #2/D TYR 106 N b2+nb60 #2/D VAL 99 C 3.981
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D VAL 99 C 4.027
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B GLU 1268 OE1 4.036
b2+nb60 #2/D TYR 106 CE2 b2+nb60 #2/B LYS 1267 NZ 4.049
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B LYS 1267 NZ 4.083
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B GLU 1268 CD 4.128
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D ILE 105 CG2 4.176
b2+nb60 #2/D TYR 106 CE2 b2+nb60 #2/B PHE 1264 CB 4.176
b2+nb60 #2/D TYR 106 CB b2+nb60 #2/D TYR 108 CZ 4.188
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D TYR 108 CE2 4.196
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/D VAL 99 O 4.229
b2+nb60 #2/D TYR 106 CE2 b2+nb60 #2/B PHE 1264 CD2 4.235
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D ALA 97 C 4.238
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D ALA 97 O 4.238
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B LYS 1267 CE 4.244
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B LYS 1267 CD 4.245
b2+nb60 #2/D TYR 106 CB b2+nb60 #2/D TYR 108 OH 4.249
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D VAL 99 N 4.255
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D VAL 99 CB 4.273
b2+nb60 #2/D TYR 106 CA b2+nb60 #2/D ILE 105 CG2 4.304
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D ILE 105 O 4.312
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D ASP 107 O 4.319
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B PHE 1264 CD2 4.326
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B GLU 1268 OE1 4.328
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D ASP 107 OD2 4.337
b2+nb60 #2/D TYR 106 CE2 b2+nb60 #2/B LYS 1267 CD 4.343
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D TYR 108 CD2 4.348
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B GLU 1268 CB 4.365
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D LYS 98 N 4.400
b2+nb60 #2/D TYR 106 CG b2+nb60 #2/D ILE 105 O 4.402
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B LYS 1267 CB 4.411
b2+nb60 #2/D TYR 106 CB b2+nb60 #2/D TYR 108 CD2 4.414
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/D GLY 101 CA 4.415
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/D SER 104 C 4.435
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D ASP 107 CG 4.445
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/D GLY 101 N 4.453
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/D GLY 101 CA 4.460
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B PHE 1264 O 4.466
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B GLU 1268 CG 4.486
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D TYR 108 CE2 4.502
b2+nb60 #2/D TYR 106 CE2 b2+nb60 #2/B LYS 1267 CE 4.514
b2+nb60 #2/D TYR 106 CG b2+nb60 #2/D TYR 108 OH 4.516
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D ASP 107 OD1 4.522
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B GLU 1268 N 4.532
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/D SER 104 C 4.542
b2+nb60 #2/D TYR 106 CG b2+nb60 #2/D VAL 99 O 4.545
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/D ILE 105 CA 4.573
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D LYS 98 CA 4.587
b2+nb60 #2/D TYR 106 CD2 b2+nb60 #2/B PHE 1264 CD2 4.590
b2+nb60 #2/D TYR 106 CD2 b2+nb60 #2/D TYR 108 OH 4.608
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/D ILE 105 O 4.609
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B PHE 1264 CD2 4.610
b2+nb60 #2/D TYR 106 N b2+nb60 #2/D VAL 99 N 4.616
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D ASP 107 OD1 4.641
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B GLU 1268 CA 4.663
b2+nb60 #2/D TYR 106 CE2 b2+nb60 #2/B PHE 1264 CG 4.663
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/B GLU 1268 OE1 4.664
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D LYS 98 CB 4.666
b2+nb60 #2/D TYR 106 CD2 b2+nb60 #2/B PHE 1264 CB 4.680
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D TYR 108 CG 4.687
b2+nb60 #2/D TYR 106 N b2+nb60 #2/D ALA 100 CA 4.750
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/B PHE 1264 CD2 4.759
b2+nb60 #2/D TYR 106 CG b2+nb60 #2/D TYR 108 CE2 4.767
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/D GLY 101 N 4.770
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D ILE 105 CA 4.778
b2+nb60 #2/D TYR 106 CA b2+nb60 #2/D TYR 108 CE2 4.794
b2+nb60 #2/D TYR 106 N b2+nb60 #2/D ALA 100 N 4.800
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B PHE 1264 CB 4.817
b2+nb60 #2/D TYR 106 CG b2+nb60 #2/D SER 104 O 4.818
b2+nb60 #2/D TYR 106 CA b2+nb60 #2/D ASP 107 O 4.826
b2+nb60 #2/D TYR 106 CA b2+nb60 #2/D VAL 99 C 4.828
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/D ILE 105 N 4.830
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D LYS 98 C 4.841
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D LYS 98 O 4.846
b2+nb60 #2/D TYR 106 C b2+nb60 #2/D VAL 99 C 4.858
b2+nb60 #2/D TYR 106 CD1 b2+nb60 #2/B PHE 1139 CZ 4.871
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B ASP 1331 OD2 4.884
b2+nb60 #2/D TYR 106 CG b2+nb60 #2/D TYR 108 CZ 4.885
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B LYS 1267 C 4.888
b2+nb60 #2/D TYR 106 N b2+nb60 #2/D VAL 99 CA 4.889
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/D ILE 105 C 4.891
b2+nb60 #2/D TYR 106 N b2+nb60 #2/D GLY 101 N 4.911
b2+nb60 #2/D TYR 106 CE2 b2+nb60 #2/B GLU 1268 OE2 4.925
b2+nb60 #2/D TYR 106 CD2 b2+nb60 #2/D ILE 105 C 4.930
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/B GLU 1268 CG 4.935
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B PHE 1264 CB 4.941
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D VAL 99 CG2 4.941
b2+nb60 #2/D TYR 106 CB b2+nb60 #2/D ASP 107 C 4.943
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D TYR 108 CA 4.944
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/D SER 104 O 4.962
b2+nb60 #2/D TYR 106 CA b2+nb60 #2/D VAL 99 N 4.981
b2+nb60 #2/D TYR 106 CG b2+nb60 #2/D ILE 105 CA 4.985
b2+nb60 #2/D TYR 106 CB b2+nb60 #2/D VAL 99 C 4.987
b2+nb60 #2/D TYR 106 CD2 b2+nb60 #2/B PHE 1264 CG 4.995
b2+nb60 #2/D TYR 106 O b2+nb60 #2/D ASP 107 OD2 4.996
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B LYS 1267 CG 4.999
124 distances
Drag select of 2 residues
> close #4
> select clear
> select #2/D:106
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/B:1264
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #2/D:99
18 atoms, 17 bonds, 2 residues, 1 model selected
> select subtract #2/B:1264
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #2/D:99
7 atoms, 6 bonds, 1 residue, 1 model selected
> select celar
Expected an objects specifier or a keyword
> select clear
> select #2/D:106
12 atoms, 12 bonds, 1 residue, 1 model selected
Drag select of 1 atoms, 4 residues
> select clear
[Repeated 1 time(s)]Drag select of 3 residues
> select clear
> select #2/D:106
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #2/B:1264
23 atoms, 23 bonds, 2 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict both distanceOnly 5.0 ignoreHiddenModels true log true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
12 distances
atom1 atom2 distance
b2+nb60 #2/D TYR 106 CE2 b2+nb60 #2/B PHE 1264 CB 4.176
b2+nb60 #2/B PHE 1264 CD2 b2+nb60 #2/D TYR 106 CE2 4.235
b2+nb60 #2/B PHE 1264 CD2 b2+nb60 #2/D TYR 106 CZ 4.326
b2+nb60 #2/D TYR 106 OH b2+nb60 #2/B PHE 1264 O 4.466
b2+nb60 #2/B PHE 1264 CD2 b2+nb60 #2/D TYR 106 CD2 4.590
b2+nb60 #2/B PHE 1264 CD2 b2+nb60 #2/D TYR 106 OH 4.610
b2+nb60 #2/B PHE 1264 CG b2+nb60 #2/D TYR 106 CE2 4.663
b2+nb60 #2/D TYR 106 CD2 b2+nb60 #2/B PHE 1264 CB 4.680
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/B PHE 1264 CD2 4.759
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B PHE 1264 CB 4.817
b2+nb60 #2/B PHE 1264 CB b2+nb60 #2/D TYR 106 OH 4.941
b2+nb60 #2/B PHE 1264 CG b2+nb60 #2/D TYR 106 CD2 4.995
12 distances
> undo
[Repeated 1 time(s)]
> ui tool show Contacts
> contacts sel restrict both interModel false intraModel false intraMol false
> log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> select clear
> select #2/B:1264@CZ
1 atom, 1 residue, 1 model selected
> select #2/B:1264@CE1
1 atom, 1 residue, 1 model selected
> select subtract #2/B:1264@CE1
Nothing selected
> select add #2/B:1264@CD1
1 atom, 1 residue, 1 model selected
> select add #2/B:1264@CE1
2 atoms, 1 residue, 1 model selected
> select add #2/B:1264@CZ
3 atoms, 1 residue, 1 model selected
> select add #2/B:1264@CE2
4 atoms, 1 residue, 1 model selected
> select add #2/B:1264@CD2
5 atoms, 1 residue, 1 model selected
> select add #2/B:1264@CG
6 atoms, 1 residue, 1 model selected
> select add #2/D:106@CD2
7 atoms, 2 residues, 1 model selected
> select add #2/D:106@CE2
8 atoms, 2 residues, 1 model selected
> select add #2/D:106@CG
9 atoms, 2 residues, 1 model selected
> select add #2/D:106@CD1
10 atoms, 2 residues, 1 model selected
> select add #2/D:106@CE1
11 atoms, 2 residues, 1 model selected
> select add #2/D:106@CZ
12 atoms, 2 residues, 1 model selected
> ui tool show Axes/Planes/Centroids
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 618, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
RuntimeError: wrapped C/C++ object of type QLabel has been deleted
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/struct_measure/tool.py", line 618, in clear_status
if s.apc_status_label.text() == s.apc_status_tip:
See log for complete Python traceback.
> ui tool show Contacts
> contacts sel restrict both interModel false intraModel false intraMol false
> log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict both interModel false intraModel false intraMol false
> log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict both interModel false intraModel false intraMol false
> log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict both intraRes true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: True
Detect intra-molecule contacts: True
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict both intraRes true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: True
Detect intra-molecule contacts: True
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict both intraRes true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: True
Detect intra-molecule contacts: True
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict both intraRes true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: True
Detect intra-molecule contacts: True
0 contacts
atom1 atom2 overlap distance
No contacts
> contacts sel restrict both distanceOnly 5.0 intraRes true log true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: True
Detect intra-molecule distances: True
6 distances
atom1 atom2 distance
b2+nb60 #2/D TYR 106 CE2 b2+nb60 #2/B PHE 1264 CD2 4.235
b2+nb60 #2/D TYR 106 CZ b2+nb60 #2/B PHE 1264 CD2 4.326
b2+nb60 #2/D TYR 106 CD2 b2+nb60 #2/B PHE 1264 CD2 4.590
b2+nb60 #2/B PHE 1264 CG b2+nb60 #2/D TYR 106 CE2 4.663
b2+nb60 #2/D TYR 106 CE1 b2+nb60 #2/B PHE 1264 CD2 4.759
b2+nb60 #2/B PHE 1264 CG b2+nb60 #2/D TYR 106 CD2 4.995
6 distances
> hide #!2 models
> show #!2 models
> ui tool show Distances
> ui tool show Contacts
> contacts sel restrict both interModel false intraModel false intraMol false
> log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> show #!5 models
> select #5/A:367@CA
1 atom, 1 residue, 1 model selected
> select #5/A:365
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:366
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #2.1 models
> show #2.1 models
> hide #2.2 models
> show #2.2 models
> hide #2.3 models
> hide #!5 models
> show #!5 models
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)
Mismatch between Cocoa '\x0' and Carbon 'x' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'X' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'x' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'X' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2248' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02db' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u2248' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u02db' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x18' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x18' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x18' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x18' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x18' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x18' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x18' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x18' for virtual key 7 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> hide #1.1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> log metadata #1
No models had metadata
> log chains #1
Chain information for b2+T4L+nb60 #1
---
Chain | Description
A B | No description available
C G | No description available
D F | No description available
> hide #!5 models
> hide #!2 models
> select #1/F:1-120
859 atoms, 875 bonds, 120 residues, 1 model selected
> select #1/D:1-120
859 atoms, 875 bonds, 120 residues, 1 model selected
> select #1/D:1-120
859 atoms, 875 bonds, 120 residues, 1 model selected
> select #1/D:1-120
859 atoms, 875 bonds, 120 residues, 1 model selected
> hide #1~sel ribbons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 ~sel ribbons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide #1 ~sel ribbons
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> select #1/C:1002-1161
1275 atoms, 1295 bonds, 160 residues, 1 model selected
> hide sel ribbons
> select #1/A:29-342
2268 atoms, 2329 bonds, 1 pseudobond, 282 residues, 2 models selected
> hide sel ribbons
> hide sel atoms
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> select #1/D:1-120
859 atoms, 875 bonds, 120 residues, 1 model selected
> select zone #1/d 5 #5/a residues true
Selected 206 atoms
> select zone #5/a 5 #1/d residues true
Selected 134 atoms
> show sel atoms
> style sel stick
Changed 134 atom styles
> select clear
> show #!2 models
> hide #!1 models
> select #2/B:1264
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:1263
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1062
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:63
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #2/B:1331
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel orange
> color sel byhetero
> label sel text D8.49
> select clear
> hide #!5 models
> hide #!2 models
> show #!2 models
> show #!5 models
> hide #!2 models
> show #!2 models
> select #5/A:64
5 atoms, 4 bonds, 1 residue, 1 model selected
> label sel text A12.49
> hide #5.2 models
> show #5.2 models
> hide #5.1 models
> select #5/A:430
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text N8.47
> select #5/A:374
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text M6.36
> hide #5.2 models
> show #5.2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #5/A:431
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:432
5 atoms, 4 bonds, 1 residue, 1 model selected
> label sel text E8.49
> ui tool show "Color Actions"
> color sel plum
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!5 models
> select #2/B:1131
11 atoms, 10 bonds, 1 residue, 1 model selected
> label sel text R3.50
> show #!5 models
> show #!1 models
> hide #!1 models
> select #5/A:132
11 atoms, 10 bonds, 1 residue, 1 model selected
> label sel text R3.50
> color sel yellow
> color sel light green
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #5/A:375
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #5/A:128
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1127
8 atoms, 7 bonds, 1 residue, 1 model selected
> select
> #2/B:868-874,924-946,949-954,957-971,974-988,990-998,1001-1021,1023-1096,1101-1136,1146-1171,1178-1187,1196-1229,1262-1299,1304-1319,1321-1327,1329-1340
2598 atoms, 2643 bonds, 1 pseudobond, 349 residues, 2 models selected
> select clear
> select #5/A:131
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/B:1130
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!5 models
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)
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)
> show sel atoms
> color sel byhetero
> show #5.1 models
> select #5/A:131
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!1 models
> hide #!5 models
> ui mousemode right zoom
> show #!5 models
> ui mousemode right select
> ui mousemode right zoom
> hide #!5 models
> hide #!2 models
> show #!1 models
> show #!5 models
> show #!2 models
> hide #!2 models
> select clear
> select #5/A:66
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #5/A:65
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/A:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:149
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5/A:139
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:148
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:147
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #5/A:148
11 atoms, 9 bonds, 2 residues, 1 model selected
> select add #5/A:146
23 atoms, 21 bonds, 3 residues, 1 model selected
> select add #5/A:145
28 atoms, 25 bonds, 4 residues, 1 model selected
Drag select of 1 residues
> select add #5/A:144
28 atoms, 29 bonds, 4 residues, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> select clear
> hide #!2 models
> ui tool show "Color Actions"
> color sel plum
[Repeated 1 time(s)]
> select #5/A:145
5 atoms, 4 bonds, 1 residue, 1 model selected
> ui tool show "Color Actions"
> color sel plum
> select #5/A:139
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select #5/A:139
7 atoms, 7 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #!2 models
> ui tool show Contacts
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> select #2/D:106
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #2/B:1264
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict both distanceOnly 5.0 intraRes true log true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: True
Detect intra-molecule distances: True
7 distances
atom1 atom2 distance
b2+nb60 #2/B PHE 1264 CD2 b2+nb60 #2/B PHE 1264 O 3.380
b2+nb60 #2/B PHE 1264 CE2 b2+nb60 #2/B PHE 1264 C 4.219
b2+nb60 #2/B PHE 1264 CD1 b2+nb60 #2/B PHE 1264 O 4.247
b2+nb60 #2/B PHE 1264 O b2+nb60 #2/B PHE 1264 CE2 4.300
b2+nb60 #2/B PHE 1264 C b2+nb60 #2/B PHE 1264 CE1 4.330
b2+nb60 #2/B PHE 1264 CZ b2+nb60 #2/B PHE 1264 C 4.674
b2+nb60 #2/B PHE 1264 CE1 b2+nb60 #2/B PHE 1264 N 4.811
7 distances
> select #2/D:106
12 atoms, 12 bonds, 1 residue, 1 model selected
> select add #2/B:1264
23 atoms, 23 bonds, 7 pseudobonds, 2 residues, 2 models selected
> ui tool show Contacts
> contacts sel restrict both intraRes true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: True
Detect intra-molecule contacts: True
1 contacts
atom1 atom2 overlap distance
b2+nb60 #2/B PHE 1264 CD2 b2+nb60 #2/B PHE 1264 O -0.200 3.380
1 contacts
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> hide #2.3 models
> show #2.3 models
> ui tool show Contacts
> contacts sel restrict both interModel false intraModel false intraMol false
> log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: False
0 contacts
atom1 atom2 overlap distance
No contacts
> select clear
> show #!1 models
> hide #!2 models
> show #!5 models
> select #1/D:102@CA
1 atom, 1 residue, 1 model selected
> select add #5/A:371
6 atoms, 4 bonds, 2 residues, 2 models selected
> ui tool show Clashes
> clashes sel restrict both distanceOnly 4.0 ignoreHiddenModels true log true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
1 distances
atom1 atom2 distance
D2+T4L #5/A ALA 371 CB b2+T4L+nb60 #1/D THR 102 CA 2.777
1 distances
> clashes sel restrict both distanceOnly 4.0 ignoreHiddenModels true log true
Ignore distances between atoms separated by 4 bonds or less
Detect intra-residue distances: False
Detect intra-molecule distances: True
1 distances
atom1 atom2 distance
D2+T4L #5/A ALA 371 CB b2+T4L+nb60 #1/D THR 102 CA 2.777
1 distances
> hide #4 models
> show #4 models
> hide #4 models
> show #6 models
> hide #6 models
> show #!2 models
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel light green
> color sel byhetero
> lebel sel text R3.50
Unknown command: lebel sel text R3.50
> label sel text R3.50
> hide #!1 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!1 models
> label sel text E6.30
> select #5/A:368
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!1 models
> hide #!2 models
> select #5/A:132
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel byelement
> undo
> color sel byhetero
> select clear
> select add #5/A:368@OE1
1 atom, 1 bond, 1 residue, 1 model selected
> select clear
> select #5/A:132@NH1
1 atom, 1 residue, 1 model selected
> select add #5/A:368@OE1
2 atoms, 2 residues, 1 model selected
> ui mousemode right distance
> distance #5/A:368@OE1 #5/A:132@NH1
Distance between D2+T4L #5/A GLU 368 OE1 and ARG 132 NH1: 3.004Å
> show #!6 models
> distance #5/A:132@NH1 #5/A:368@OE1
Distance already exists; modify distance properties with 'distance style'
> ~distance #5/A:368@OE1 #5/A:132@NH1
> distance #5/A:368@OE1 #5/A:132@NH2
Distance already exists; modify distance properties with 'distance style'
> distance #5/A:368@OE1 #5/A:132@NH2
Distance already exists; modify distance properties with 'distance style'
> show #!2 models
> select clear
> hide #6 models
> show #6 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> show #!5 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> ui mousemode right zoom
> select #5/A:367
5 atoms, 4 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> select #2/B:1137
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #2/B:1138
7 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!2 models
> hide #6 models
> hide #!5 models
> show #!2 models
> hide #!1 models
> show #!1 models
> show #!5 models
> hide #!2 models
> select #5/A:132
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5/A:129-138
77 atoms, 77 bonds, 10 residues, 1 model selected
> select clear
> select #5/A:133
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:133
12 atoms, 12 bonds, 1 residue, 1 model selected
> show #!2 models
> hide #!2 models
> show #6 models
> show #!2 models
> hide #!5 models
> hide #!1 models
> select #2/B:1269
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:1131
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #2/B:1268
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #2/B:1264
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #2/B:1264
11 atoms, 11 bonds, 1 residue, 1 model selected
> show #!5 models
> hide #!2 models
> hide #!5 models
> hide #6 models
> show #3 models
> close #7
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!5 models
> select #3/A:152
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #3/A:151-155
42 atoms, 41 bonds, 5 residues, 1 model selected
> select #3/A:130-155
218 atoms, 222 bonds, 26 residues, 1 model selected
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)
> show sel atoms
> select clear
> select #5/A:131
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:131-157
167 atoms, 168 bonds, 1 pseudobond, 23 residues, 2 models selected
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)
> show sel atoms
> select clear
> select #3/A:132
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #5/A:135
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:134
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #3/A:137
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #3/A:137
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/A:156
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #4 models
> hide #4 models
> show #6 models
> hide #6 models
> show #3 models
> select #5/A:154
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #5/A:133-154
126 atoms, 127 bonds, 1 pseudobond, 18 residues, 2 models selected
> open "/Users/sqx/Documents/Lab/work/Project/D2R【202209】/Nb6
> construct/D2R6-2(15).cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore
self.reset()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state
task.terminate()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
AttributeError: 'Tasks' object has no attribute 'remove'
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore
self.reset()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state
task.terminate()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
AttributeError: 'Tasks' object has no attribute 'remove'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 245, in event
_open_dropped_file(self.session, event.file())
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1915, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 458, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1001, in open
session.restore(stream, path=path, resize_window=resize_window)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 739, in restore
self.reset()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state
task.terminate()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
AttributeError: 'Tasks' object has no attribute 'remove'
AttributeError: 'Tasks' object has no attribute 'remove'
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
See log for complete Python traceback.
> open "/Users/sqx/Documents/Lab/work/Project/D2R【202209】/Nb6
> construct/D2R6-3(OUT).cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore
self.reset()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state
task.terminate()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
AttributeError: 'Tasks' object has no attribute 'remove'
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore
self.reset()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state
task.terminate()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
AttributeError: 'Tasks' object has no attribute 'remove'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 245, in event
_open_dropped_file(self.session, event.file())
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1915, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 458, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1001, in open
session.restore(stream, path=path, resize_window=resize_window)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 739, in restore
self.reset()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state
task.terminate()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
AttributeError: 'Tasks' object has no attribute 'remove'
AttributeError: 'Tasks' object has no attribute 'remove'
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
See log for complete Python traceback.
> open "/Users/sqx/Documents/Lab/work/Project/D2R【202209】/Nb6
> construct/D2R6-1(31).cxs"
Unable to restore session, resetting.
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore
self.reset()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state
task.terminate()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
AttributeError: 'Tasks' object has no attribute 'remove'
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 697, in restore
self.reset()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state
task.terminate()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
AttributeError: 'Tasks' object has no attribute 'remove'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 245, in event
_open_dropped_file(self.session, event.file())
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1915, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 458, in collated_open
return remember_data_format()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format
models, status = func(*func_args, **func_kw)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 1001, in open
session.restore(stream, path=path, resize_window=resize_window)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 739, in restore
self.reset()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 541, in reset
sm.reset_state(container, self)
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 547, in reset_state
task.terminate()
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
AttributeError: 'Tasks' object has no attribute 'remove'
AttributeError: 'Tasks' object has no attribute 'remove'
File
"/Applications/ChimeraX_techpreview.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tasks.py", line 155, in terminate
self.session.tasks.remove(self)
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 76.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,3
Chip: Apple M1 Pro
Total Number of Cores: 8 (6 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 7429.41.5
OS Loader Version: 7429.41.5
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 22 days 8:47
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 14
Vendor: Apple (0x106b)
Metal Family: Supported, Metal GPUFamily Apple 7
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.0.8
Babel: 2.10.3
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.1
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.2.4
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.5.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41
ChimeraX-AtomicLibrary: 7.0.2
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3
ChimeraX-ChangeChains: 1.0
ChimeraX-CheckWaters: 1.1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.1
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5.dev202208200154
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.3
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.6
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.7
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
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: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.9
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.23
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.3
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 0.10.0
filelock: 3.7.1
fonttools: 4.36.0
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.33
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 4.12.0
ipykernel: 6.15.1
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 4.11.1
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.5
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.3
numpy: 1.23.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.1
pkginfo: 1.8.3
prompt-toolkit: 3.0.30
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.1
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.1
python-dateutil: 2.8.2
pytz: 2022.2.1
pyzmq: 23.2.1
qtconsole: 5.3.1
QtPy: 2.2.0
RandomWords: 0.3.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 63.3.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.4.0
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
urllib3: 1.26.11
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.8.1
Change History (2)
comment:1 by , 3 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session reset: 'Tasks' object has no attribute 'remove' |
comment:2 by , 3 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Duplicate of #7602