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Opened 4 years ago
Last modified 4 years ago
#4586 assigned defect
Session restore: _pickle.UnpicklingError: invalid load key
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> Mono vs Dimers/r3md_v2.cxs"
restore_snapshot for "RotamerRestraintMgr" returned None
restore_snapshot for "RotamerRestraintMgr" returned None
Log from Thu Mar 11 14:35:25 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> Mono vs Dimers/r3md.cxs"
Log from Thu Mar 11 13:06:46 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/kkkkk.cif"
Chain information for kkkkk.cif #1
---
Chain | Description
A | DNA-directed RNA polymerase I subunit RPA190
B | DNA-directed RNA polymerase I subunit RPA135
C | DNA-directed RNA polymerases I and III subunit RPAC1
D | DNA-directed RNA polymerase I subunit RPA14
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
G | DNA-directed RNA polymerase I subunit RPA43
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I | DNA-directed RNA polymerase I subunit RPA12
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K | DNA-directed RNA polymerases I and III subunit RPAC2
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
M | DNA-directed RNA polymerase I subunit RPA49
N | DNA-directed RNA polymerase I subunit RPA34
O | RNA polymerase I-specific transcription initiation factor RRN3
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/polI-Rrn3.mrc"
Opened polI-Rrn3.mrc, grid size 128,128,128, pixel 2.16, shown at level 0.142,
step 1, values float32
> volume #2 level 0.06612
> transparency 50
> select #1
74764 atoms, 75502 bonds, 48 pseudobonds, 4693 residues, 3 models selected
> hide sel cartoons
> hide sel atoms
> show sel cartoons
> volume #2 level 0.1178
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/PolIRrn3fittes_complete.cif"
Chain information for PolIRrn3fittes_complete.cif #3
---
Chain | Description
A | DNA-directed RNA polymerase I subunit RPA190
B | DNA-directed RNA polymerase I subunit RPA135
C | DNA-directed RNA polymerases I and III subunit RPAC1
D | DNA-directed RNA polymerase I subunit RPA14
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
G | DNA-directed RNA polymerase I subunit RPA43
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I | DNA-directed RNA polymerase I subunit RPA12
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K | DNA-directed RNA polymerases I and III subunit RPAC2
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
M | DNA-directed RNA polymerase I subunit RPA49
N | DNA-directed RNA polymerase I subunit RPA34
O | RNA polymerase I-specific transcription initiation factor RRN3
> hide sel atoms
> show sel cartoons
> select #3
74764 atoms, 75502 bonds, 48 pseudobonds, 4693 residues, 3 models selected
> hide sel atoms
> show sel cartoons
> close #1
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/PolIRrn3fittes_complete.cif"
Chain information for PolIRrn3fittes_complete.cif #1
---
Chain | Description
A | DNA-directed RNA polymerase I subunit RPA190
B | DNA-directed RNA polymerase I subunit RPA135
C | DNA-directed RNA polymerases I and III subunit RPAC1
D | DNA-directed RNA polymerase I subunit RPA14
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
G | DNA-directed RNA polymerase I subunit RPA43
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I | DNA-directed RNA polymerase I subunit RPA12
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K | DNA-directed RNA polymerases I and III subunit RPAC2
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
M | DNA-directed RNA polymerase I subunit RPA49
N | DNA-directed RNA polymerase I subunit RPA34
O | RNA polymerase I-specific transcription initiation factor RRN3
> close #3
> hide atoms
> show cartoons
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/script-
> domainssattributionpolI-030720envoyeMichael.cxc"
> hide atoms
> show cartoons
> select all
74764 atoms, 75502 bonds, 48 pseudobonds, 4693 residues, 5 models selected
> color sel grey
> select clear
> name rpa190 #1/A
> name rpa135 #1/B
> name rpb5 #1/E
> name rpb6 #1/F
> name rpb8 #1/H
> name rpb10 #1/J
> name rpb12 #1/L
> name ac40 #1/C
> name ac19 #1/K
> name rpa12 #1/I
> name rpa14 #1/D
> name rpa43 #1/G
> name rpa34 #1/N
> name rpa49 #1/M
> name a++clamp #1/A:01-90 #1/A:356-477 #1/A:1608-1664 #1/A:126-303
> #1/B:1170-1203
> name a++jaw #1/A:1285-1320 #1/A:1456-1500 #1/E:1-145 #1/I:1-39
> name a++stalk #1/D #1/G
> name a++shelf #1/A:477-506 #1/A:581-654 #1/A:506-581 #1/A:1060-1137
> #1/A:991-1053 #1/A:1180-1261 #1/A:1514-1608 #1/E #1/F #1/B:1068-1092
> name a++core #1/B:647-698 #1/H #1/A:709-827 #1/A:827-991 #1/B:469-553
> #1/B:698-800 #1/C #1/J #1/K #1/B:43-209 #1/B:400-469 #1/L #1/B:800-910
> name rpa190++clampcore++engel #1/A:01-90 #1/A:356-477 #1/A:1608-1664
> name rpa190++clampcore++tornero #1/A:01-90 #1/A:350-477 #1/A:1608-1664
> name rpa190++clamphead++engel #1/A:126-303
> name rpa190++clamphead++tornero #1/A:90-350
> name rpa190++activesite #1/A:477-506 #1/A:581-654
> name rpa190++dock #1/A:506-581
> name rpa190++pore++engel #1/A:709-827
> name rpa190++pore++tornero #1/A:654-828
> name rpa190++funnel #1/A:827-991
> name rpa190++cleft++engel #1/A:991-1053 #1/A:1180-1261 #1/A:1514-1608
> name rpa190++cleft++tornero #1/A:991-1051 #1/A:1180-1260 #1/A:1499-1607
> name rpa190++foot #1/A:1060-1137
> name rpa190++jaw++engel #1/A:1285-1320 #1/A:1456-1500
> name rpa190++jaw++tornero #1/A:1260-1360 #1/A:1400-1499
> name rpa190++expander++engel #1/A:1337-1440
> name rpa190++mimickingloop++tornero #1/A:1360-1400
> name rpa190++BH++engel #1/A:991-1051
> name rpa190++BH++Darriere #1/A:1012-1016
> name rpa135++extendedprotrusion #1/B:1-43
> name rpa135++nter #1/B:1-42
> name rpa135++protrusion++engel #1/B:43-209 #1/B:400-469
> name rpa135++protrusion++tornero #1/B:42-210 #1/B:399-470
> name rpa135++lobe++engel #1/B:209-400
> name rpa135++lobe++tornero #1/B:210-399
> name rpa135++fork++engel #1/B:469-553
> name rpa135++fork++tornero #1/B:470-553
> name rpa135++external1++engel #1/B:647-698
> name rpa135++external1++tornero #1/B:649-697
> name rpa135++external2++engel #1/B:553-647
> name rpa135++external2++tornero #1/B:553-649
> name rpa135++hybridbinding++engel #1/B:698-800
> name rpa135++hybridbinding++tornero #1/B:697-800
> name rpa135++wall++engel #1/B:800-910
> name rpa135++wall++tornero #1/B:800-911
> name rpa135++anchor++engel #1/B:1068-1092
> name rpa135++anchor++tornero #1/B:1069-1095
> name rpa135++stalkbinding++tornero #1/B:1095-1170
> name rpa135++clamp++engel #1/B:1092-1203
> name rpa135++clamp++tornero #1/B:1170-1203
> name rpb5++jaw #1/E:1-145
> name rpb5++assembly #1/E:145-215
> name rpb6++tail #1/F:01-72
> name rpb6++assembly #1/F:72-155
> name rpb6++nter++tornero #1/F:55-71
> name rpb8++betabarrel #1/H:01-63 #1/H:96-146
> name rpb8++loop #1/H:63-96
> name rpb10++zincbundle #1/J:1-53
> name rpb10++tail #1/J:53-70
> name rpb12++zincribbon #1/L:1-60
> name rpb12++tail #1/L:60-70
> name ac19++tail #1/K:1-48
> name ac19++dimerization #1/K:49-142
> name ac40++nterextension #1/C:1-31
> name ac40++dimerization #1/C:31-75 #1/C:220-230 #1/C:297-335
> name ac40++domain2 #1/C:75-143 #1/C:168-220
> name ac40++zincloop #1/C:143-168
> name ac40++looptoe #1/C:230-297
> name rpa12++jaw++zincbindingribbon1 #1/I:1-40
> name rpa12++linkerflexible #1/I:40-65
> name rpa12++zincbindingribbon2 #1/I:65-125
> name rpa43++nter #1/G:1-37
> name rpa43++tipdomain #1/G:38-91
> name rpa43++tiploop #1/G:92-113
> name rpa43++obdomain #1/G:114-248
> name rpa43++ctail #1/G:249-326
> name rpa43++connector #1/G:270-313
> name rpa14++nter #1/D:1-21
> name rpa14++tipassociateddomain #1/D:22-96
> name rpa14++linker #1/D:97-137
> name rpa49++nterdimerization #1/M:1-101
> name rpa49++linkerdomain #1/M:102-184
> name rpa49++twh #1/M:185-403
> name rpa49++wh1 #1/M:255-320
> name rpa49++wh2 #1/M:321-403
> name rpa49++cter #1/M:403-415
> name rpa34++nter #1/N:1-22
> name rpa34++dimerizationdomain #1/N:23-144
> name rpa34++ctail #1/N:145-233
executed script-domainssattributionpolI-030720envoyeMichael.cxc
> ui tool show "Basic Actions"
QWindowsWindow::setGeometry: Unable to set geometry 458x195+1511+651 (frame:
476x242+1502+613) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 575x246+1512+658 (frame:
593x293+1503+620) margins: 9, 38, 9, 9 minimum size: 89x1 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=107,48
maxtrack=524305,524334)
> select #1/o
7618 atoms, 7704 bonds, 2 pseudobonds, 463 residues, 2 models selected
> ui tool show "Color Actions"
> color sel red
> color sel red
> lighting soft
> lighting full
> lighting simple
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting simple
> volume #2 level 0.1046
> select #1/o:551
24 atoms, 23 bonds, 1 residue, 1 model selected
> select #1/o:555
Nothing selected
> select #1/o:552
Nothing selected
> select #1/o:551
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> select #1/o:552
Nothing selected
> select #1/o:551
24 atoms, 23 bonds, 1 residue, 1 model selected
> distance #1/o:551
Expected exactly two atoms and/or measurable objects (e.g. axes, planes), got
24
> distance #1/o:551@ca #1/a:582@◘ca
Expected a keyword
> distance #1/o:551@ca #1/a:582@ca
Distance between /O ARG 551 CA and /A LYS 582 CA: 33.108Å
> distance #1/o:551@ca #1/c:329@ca
Distance between /O ARG 551 CA and /C LYS 329 CA: 13.171Å
> distance style radius 0.11
> distance style radius 0.11
> distance style radius 0.12
> distance style radius 0.12
> distance style radius 0.13
> distance style radius 0.13
> distance style radius 0.14
> distance style radius 0.14
> distance style radius 0.15
> distance style radius 0.15
> distance style radius 0.16
> distance style radius 0.16
> distance style radius 0.17
> distance style radius 0.17
> distance style radius 0.18
> distance style radius 0.18
> distance style radius 0.19
> distance style radius 0.19
> distance style radius 0.2
> distance style radius 0.2
> distance style radius 0.21
> distance style radius 0.21
> distance style radius 0.22
> distance style radius 0.22
> distance style radius 0.23
> distance style radius 0.23
> distance style radius 0.24
> distance style radius 0.24
> distance style radius 0.25
> distance style radius 0.25
> distance style radius 0.26
> distance style radius 0.26
> distance style radius 0.27
> distance style radius 0.27
> distance style radius 0.28
> distance style radius 0.28
> distance style radius 0.29
> distance style radius 0.29
> distance style radius 0.3
> distance style radius 0.3
> distance style radius 0.31
> distance style radius 0.31
> distance style radius 0.32
> distance style radius 0.32
> distance style dashes 10
> distance style dashes 10
> distance style dashes 9
> distance style dashes 9
> distance style dashes 10
> distance style dashes 10
> distance style dashes 9
> distance style dashes 9
> distance style decimalPlaces 2
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> distance style decimalPlaces 1
> view sel
> distance style radius 0.33
> distance style radius 0.33
> distance style radius 0.34
> distance style radius 0.34
> distance style radius 0.35
> distance style radius 0.35
> distance style radius 0.36
> distance style radius 0.36
> distance style radius 0.37
> distance style radius 0.37
> distance style radius 0.38
> distance style radius 0.38
> distance style radius 0.39
> distance style radius 0.39
> distance style radius 0.4
> distance style radius 0.4
> distance style radius 0.41
> distance style radius 0.41
> distance style radius 0.42
> distance style radius 0.42
> distance style radius 0.43
> distance style radius 0.43
> distance style radius 0.44
> distance style radius 0.44
> distance style radius 0.45
> distance style radius 0.45
> distance style radius 0.46
> distance style radius 0.46
> distance style radius 0.47
> distance style radius 0.47
> distance style radius 0.48
> distance style radius 0.48
> distance style radius 0.49
> distance style radius 0.49
> distance style radius 0.5
> distance style radius 0.5
> distance style radius 0.51
> distance style radius 0.51
> distance style radius 0.52
> distance style radius 0.52
> distance style radius 0.53
> distance style radius 0.53
> distance style radius 0.54
> distance style radius 0.54
> distance style radius 0.55
> distance style radius 0.55
> distance style radius 0.56
> distance style radius 0.56
> distance style radius 0.57
> distance style radius 0.57
> distance style radius 0.58
> distance style radius 0.58
> distance style radius 0.59
> distance style radius 0.59
> distance style radius 0.6
> distance style radius 0.6
> distance style radius 0.61
> distance style radius 0.61
> distance style radius 0.62
> distance style radius 0.62
> distance style radius 1
> distance style radius 1
> distance style radius 1
> distance #1/o:551@ca #1/c:329@ca
Distance already exists; modify distance properties with 'distance style'
> ui tool show "Side View"
QWindowsWindow::setGeometry: Unable to set geometry 458x116+3254+649 (frame:
474x155+3246+618) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY1". Resulting geometry: 572x123+3254+649 (frame:
588x162+3246+618) margins: 8, 31, 8, 8 minimum size: 572x123 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=588,162
maxtrack=524303,524326)
QWindowsWindow::setGeometry: Unable to set geometry 572x123+1439+519 (frame:
590x170+1430+481) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 717x156+1440+526 (frame:
735x203+1431+488) margins: 9, 38, 9, 9 minimum size: 572x123 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=590,170
maxtrack=524305,524334)
> distance style symbol false
> distance style symbol true
> distance style radius 0
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 389, in <lambda>
self._float_widget.valueChanged.connect(lambda val, s=self: s.make_callback())
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 170, in make_callback
self._callback(self)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\dist_monitor\settings.py", line 72, in _opt_cb
val = opt.value
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 371, in get_value
val = self._float_widget.value()
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 886, in value
step = singleStep()
NameError: name 'singleStep' is not defined
NameError: name 'singleStep' is not defined
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\ui\options\options.py", line 886, in value
step = singleStep()
See log for complete Python traceback.
> distance style radius 0.01
> distance style radius 0.01
> distance style radius 0.02
> distance style radius 0.02
> distance style radius 0.03
> distance style radius 0.03
> distance style radius 0.04
> distance style radius 0.04
> distance style radius 0.05
> distance style radius 0.05
> distance style radius 0.06
> distance style radius 0.06
> distance style radius 0.07
> distance style radius 0.07
> distance style radius 0.08
> distance style radius 0.08
> distance style radius 0.09
> distance style radius 0.09
> distance style radius 0.1
> distance style radius 0.1
> distance style radius 0.11
> distance style radius 0.11
> distance style radius 0.12
> distance style radius 0.12
> distance style radius 0.13
> distance style radius 0.13
> distance style radius 0.14
> distance style radius 0.14
> distance style radius 0.15
> distance style radius 0.15
> distance style radius 0.16
> distance style radius 0.16
> distance style radius 0.17
> distance style radius 0.17
> distance style radius 0.18
> distance style radius 0.18
> distance style radius 0.19
> distance style radius 0.19
> distance style radius 0.2
> distance style radius 0.2
> distance style radius 0.21
> distance style radius 0.21
> distance style radius 0.22
> distance style radius 0.22
> distance style radius 0.23
> distance style radius 0.23
> distance style radius 0.24
> distance style radius 0.24
> distance style radius 0.25
> distance style radius 0.25
> distance style radius 0.26
> distance style radius 0.26
> distance style radius 0.27
> distance style radius 0.27
> distance style radius 0.28
> distance style radius 0.28
> distance style radius 0.29
> distance style radius 0.29
> distance style radius 0.3
> distance style radius 0.3
> distance style radius 0.31
> distance style radius 0.31
> distance style radius 0.32
> distance style radius 0.32
> distance style radius 0.33
> distance style radius 0.33
> distance style radius 0.34
> distance style radius 0.34
> distance style radius 0.35
> distance style radius 0.35
> distance style radius 0.36
> distance style radius 0.36
> distance style radius 0.37
> distance style radius 0.37
> distance style radius 0.38
> distance style radius 0.38
> distance style radius 0.39
> distance style radius 0.39
> distance style symbol false
> distance style symbol true
> distance style symbol false
> distance style symbol true
> select #1/c:329@ca
1 atom, 1 residue, 1 model selected
> select #1/c:329
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> color sel blue
> select #1/a:582
22 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 22 atom styles
> style sel ball
Changed 22 atom styles
> color sel blue
> select #1/c:329
22 atoms, 21 bonds, 1 residue, 1 model selected
> style sel ball
Changed 22 atom styles
> select #1/o
7618 atoms, 7704 bonds, 2 pseudobonds, 463 residues, 2 models selected
> ui tool show "Color Actions"
> color sel red
> color sel red
> color (#!1 & sel) #aa0000ff
> lighting flat
> lighting soft
> select #1
74764 atoms, 75502 bonds, 50 pseudobonds, 4693 residues, 4 models selected
> ~select #1
Nothing selected
> volume #2 level 0.1162
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting soft
> lighting soft
> select #1/o
7618 atoms, 7704 bonds, 2 pseudobonds, 463 residues, 2 models selected
> select #3
2 pseudobonds, 2 models selected
> select #1/o
7618 atoms, 7704 bonds, 2 pseudobonds, 463 residues, 2 models selected
> ui tool show "Color Actions"
> select #1
74764 atoms, 75502 bonds, 50 pseudobonds, 4693 residues, 4 models selected
> select #3
2 pseudobonds, 2 models selected
> select #1/o
7618 atoms, 7704 bonds, 2 pseudobonds, 463 residues, 2 models selected
> view sel
> color (#!1 & sel) #aa007fff
> color (#!1 & sel) #aa0000ff
> ui tool show "Basic Actions"
> select rpa190++dock
1184 atoms, 1195 bonds, 76 residues, 1 model selected
> view sel
> volume #2 color #7e7e7e80
> volume #2 color #7f7f7f80
> volume #2 color #83838380
> volume #2 color #95959580
> volume #2 color #96969680
> volume #2 color #9a9a9a80
> volume #2 color #9c9c9c80
> volume #2 color #9d9d9d80
> volume #2 color #9f9f9f80
> volume #2 color #aaaaaa80
> volume #2 color #b0b0b080
> volume #2 color #b9b9b980
> volume #2 color #bcbcbc80
> volume #2 color #c5c5c580
> volume #2 color #c6c6c680
> volume #2 color #c5c5c580
> volume #2 color #c3c3c380
> volume #2 color #c2c2c280
> volume #2 color #c1c1c180
> volume #2 color #bababa80
> volume #2 color #b9b9b980
> volume #2 color #b8b8b880
> volume #2 color #b6b6b680
> volume #2 color #b5b5b580
> volume #2 color #b4b4b480
> volume #2 color #b3b3b380
> volume #2 color #b1b1b180
> volume #2 color #acacac80
> volume #2 color #ababab80
> volume #2 color #aaaaaa80
> volume #2 color #a6a6a680
> volume #2 color #a3a3a380
> volume #2 color #8b8b8b80
> volume #2 color #63636380
> volume #2 color #61616180
> volume #2 color #62626280
> volume #2 color #63636380
> volume #2 color #64646480
> volume #2 color #66666680
> volume #2 color #67676780
> volume #2 color #6d6d6d80
> volume #2 color #70707080
> volume #2 color #78787880
> volume #2 color #7d7d7d80
> volume #2 color #8b8b8b80
> volume #2 color #8c8c8c80
> volume #2 color #94949480
> volume #2 color #96969680
> volume #2 color #98989880
> volume #2 color #99999980
> volume #2 color #9a9a9a80
> volume #2 color #9f9f9f80
> volume #2 color #a3a3a380
> volume #2 color #a5a5a580
> volume #2 color #a6a6a680
> volume #2 color #a8a8a880
> volume #2 color #ababab80
> volume #2 color #adadad80
> volume #2 color #afafaf80
> volume #2 color #b0b0b080
> volume #2 color #b4b4b480
> volume #2 color #b6b6b680
> volume #2 color #b8b8b880
> volume #2 color #b9b9b980
> volume #2 color #b8b8b880
> volume #2 color #b9b9b980
> volume #2 color #bababa80
> volume #2 color #bcbcbc80
> volume #2 color #bdbdbd80
> view sel
> color sel #00aa7fff
> hide #!1 models
> show #!1 models
> select #1
74764 atoms, 75502 bonds, 50 pseudobonds, 4693 residues, 4 models selected
> ~select #1
Nothing selected
> select #1/o:551
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> view sel
> volume #2 level 0.1246
> select #1/c
4836 atoms, 4888 bonds, 305 residues, 1 model selected
> color sel lime
> select #1/d
923 atoms, 929 bonds, 1 pseudobond, 58 residues, 2 models selected
> select #1/k
1583 atoms, 1594 bonds, 101 residues, 1 model selected
> color sel yellow
> select #1/c:329
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel medium blue
> select #1/a:582
22 atoms, 21 bonds, 1 residue, 1 model selected
> color sel blue
> select #1/a:582
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #1
74764 atoms, 75502 bonds, 50 pseudobonds, 4693 residues, 4 models selected
> ~select #1
Nothing selected
> volume #2 level 0.1015
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/Figure Fit
> PolI.cxs"
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/Fit
> PolIRrn3.png" width 1340 height 820 supersample 3
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> lighting simple
> lighting flat
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting full
> graphics silhouettes false
> lighting full
> lighting full
> lighting flat
> lighting full
> graphics silhouettes false
> lighting full
> lighting flat
> lighting full
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I
> Maps/4c2m_2_monomers.cif"
Chain information for 4c2m_2_monomers.cif #4
---
Chain | Description
A | DNA-directed RNA polymerase I subunit RPA190
B | DNA-directed RNA polymerase I subunit RPA135
C | DNA-directed RNA polymerases I and III subunit RPAC1
D | DNA-directed RNA polymerase I subunit RPA14
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
G O | DNA-directed RNA polymerase I subunit RPA43
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I | DNA-directed RNA polymerase I subunit RPA12
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K | DNA-directed RNA polymerases I and III subunit RPAC2
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
M | DNA-directed RNA polymerase I subunit RPA49
N | DNA-directed RNA polymerase I subunit RPA34
4c2m_2_monomers.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> view
> view
> mmaker #4 to #2
No 'to' model specified
> mmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PolIRrn3fittes_complete.cif, chain A (#1) with 4c2m_2_monomers.cif,
chain A (#4), sequence alignment score = 8154
RMSD between 1302 pruned atom pairs is 1.024 angstroms; (across all 1480
pairs: 1.505)
> view
> hide cartoons
> hide atoms
> show cartoons
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> mmaker #4/b to #1/b
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PolIRrn3fittes_complete.cif, chain B (#1) with 4c2m_2_monomers.cif,
chain B (#4), sequence alignment score = 6116.9
RMSD between 1041 pruned atom pairs is 0.638 angstroms; (across all 1174
pairs: 1.364)
> show #!4 models
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/Dimmers vs
> PolIRrn3.cxs"
> ui tool show Distances
> ui tool show Matchmaker
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PolIRrn3fittes_complete.cif, chain A (#1) with 4c2m_2_monomers.cif,
chain A (#4), sequence alignment score = 8154
RMSD between 1302 pruned atom pairs is 1.024 angstroms; (across all 1480
pairs: 1.505)
> mmaker #4/b to #1/b
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PolIRrn3fittes_complete.cif, chain B (#1) with 4c2m_2_monomers.cif,
chain B (#4), sequence alignment score = 6116.9
RMSD between 1041 pruned atom pairs is 0.638 angstroms; (across all 1174
pairs: 1.364)
> matchmaker #!4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PolIRrn3fittes_complete.cif, chain A (#1) with 4c2m_2_monomers.cif,
chain A (#4), sequence alignment score = 8154
RMSD between 1302 pruned atom pairs is 1.024 angstroms; (across all 1480
pairs: 1.505)
> mmaker #4/b to #1/b
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PolIRrn3fittes_complete.cif, chain B (#1) with 4c2m_2_monomers.cif,
chain B (#4), sequence alignment score = 6116.9
RMSD between 1041 pruned atom pairs is 0.638 angstroms; (across all 1174
pairs: 1.364)
> select a++core
23937 atoms, 24164 bonds, 11 pseudobonds, 1514 residues, 3 models selected
> select a++core
23937 atoms, 24164 bonds, 11 pseudobonds, 1514 residues, 3 models selected
> mmaker #4 to a++core
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 PolIRrn3fittes_complete.cif, chain B (#1) with 4c2m_2_monomers.cif,
chain B (#4), sequence alignment score = 2940.3
RMSD between 580 pruned atom pairs is 0.605 angstroms; (across all 580 pairs:
0.605)
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/yvcx.cxs"
> morph
Missing or invalid "structures" argument: empty atom specifier
> morph #1,4
Computed 21 frame morph #5
> coordset #5 1,21
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!1 models
> hide #5.2 models
> hide #5.1 models
> hide #!3 models
> hide #!2 models
> select #1
74764 atoms, 75502 bonds, 50 pseudobonds, 4693 residues, 4 models selected
> ~select #1
Nothing selected
> select #5
33728 atoms, 34386 bonds, 17 pseudobonds, 4256 residues, 2 models selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!5 models
> close #5
> delete #4/o
> morph #1,4
models have different number of chains, 15 (Morph -
PolIRrn3fittes_complete.cif #/A,Morph - PolIRrn3fittes_complete.cif #/B,Morph
- PolIRrn3fittes_complete.cif #/C,Morph - PolIRrn3fittes_complete.cif
#/D,Morph - PolIRrn3fittes_complete.cif #/E,Morph -
PolIRrn3fittes_complete.cif #/F,Morph - PolIRrn3fittes_complete.cif #/G,Morph
- PolIRrn3fittes_complete.cif #/H,Morph - PolIRrn3fittes_complete.cif
#/I,Morph - PolIRrn3fittes_complete.cif #/J,Morph -
PolIRrn3fittes_complete.cif #/K,Morph - PolIRrn3fittes_complete.cif #/L,Morph
- PolIRrn3fittes_complete.cif #/M,Morph - PolIRrn3fittes_complete.cif
#/N,Morph - PolIRrn3fittes_complete.cif #/O) and 14 (4c2m_2_monomers.cif
#4/A,4c2m_2_monomers.cif #4/B,4c2m_2_monomers.cif #4/C,4c2m_2_monomers.cif
#4/D,4c2m_2_monomers.cif #4/E,4c2m_2_monomers.cif #4/F,4c2m_2_monomers.cif
#4/G,4c2m_2_monomers.cif #4/H,4c2m_2_monomers.cif #4/I,4c2m_2_monomers.cif
#4/J,4c2m_2_monomers.cif #4/K,4c2m_2_monomers.cif #4/L,4c2m_2_monomers.cif
#4/M,4c2m_2_monomers.cif #4/N)
> undo
> undo
> undo
> undo
> undo
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I
> Maps/4c2m_2_monomers.cif"
Chain information for 4c2m_2_monomers.cif #5
---
Chain | Description
A | DNA-directed RNA polymerase I subunit RPA190
B | DNA-directed RNA polymerase I subunit RPA135
C | DNA-directed RNA polymerases I and III subunit RPAC1
D | DNA-directed RNA polymerase I subunit RPA14
E | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
G O | DNA-directed RNA polymerase I subunit RPA43
H | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I | DNA-directed RNA polymerase I subunit RPA12
J | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K | DNA-directed RNA polymerases I and III subunit RPAC2
L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
M | DNA-directed RNA polymerase I subunit RPA49
N | DNA-directed RNA polymerase I subunit RPA34
4c2m_2_monomers.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> mmaker #5/b to #1/b
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker PolIRrn3fittes_complete.cif, chain B (#1) with 4c2m_2_monomers.cif,
chain B (#5), sequence alignment score = 6116.9
RMSD between 1041 pruned atom pairs is 0.638 angstroms; (across all 1174
pairs: 1.364)
> hide #!1,5 atoms
> show #!1,5 cartoons
> select #5/o
414 atoms, 417 bonds, 53 residues, 1 model selected
> select #5/o
414 atoms, 417 bonds, 53 residues, 1 model selected
> 265-301
Unknown command: 265-301
> select #5/o
414 atoms, 417 bonds, 53 residues, 1 model selected
> 265
Unknown command: 265
> select #5/o:265
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/o:265-301
294 atoms, 297 bonds, 37 residues, 1 model selected
> select #5/o:265-316
413 atoms, 417 bonds, 52 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #1/O
Alignment identifier is 1/O
> delete #5/o:267-316
No statusbar messages will be shown due to inadequate OpenGL
> morph #1,5
Computed 21 frame morph #6
> coordset #6 1,21
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/moph PolIRrn3
> Dimmer.cxs"
> hide #!6 models
> show #!6 models
> select #6
33545 atoms, 34203 bonds, 17 pseudobonds, 4225 residues, 2 models selected
> hide #!6 models
> show #!1 models
> show #!5 models
> show #!6 models
> show #!2 models
> ~select #6
Nothing selected
> nucleotides #!1,5-6 atoms
> style nucleic & #!1,5-6 stick
Changed 0 atom styles
> select #1
74764 atoms, 75502 bonds, 50 pseudobonds, 4693 residues, 4 models selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> hide #!6 models
> hide #!2 models
> hide #!1 models
> select #5
34302 atoms, 34772 bonds, 42 pseudobonds, 4491 residues, 3 models selected
> nucleotides sel fill
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel tube/slab shape box
> nucleotides sel ladder
> style sel stick
Changed 34302 atom styles
> hide sel cartoons
> show sel cartoons
> cartoon style (#!5 & sel) modeHelix tube sides 20
> cartoon style (#!5 & sel) xsection oval modeHelix default
> cartoon style (#!5 & sel) xsection rectangle modeHelix default
> cartoon style (#!5 & sel & coil) xsection oval
> cartoon style (#!5 & sel) xsection barbell modeHelix default
> cartoon style (#!5 & sel) modeHelix tube sides 20
> show #!1 models
> cartoon style (#!5 & sel) xsection oval modeHelix default
> ~select #5
Nothing selected
> show #!2 models
> volume #2 style mesh
> volume #2 style surface
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/morph PolIRrn3
> Dimers.cxs"
> volume #2 color #bebebe80
> volume #2 color #bfbfbf80
> volume #2 color #d6d6d680
> volume #2 color #e3e3e380
> volume #2 color #e5e5e580
> volume #2 color #e6e6e680
> volume #2 color #e7e7e780
> volume #2 color #ebebeb80
> volume #2 color #f4f4f480
> volume #2 color #ffffff80
> volume #2 color #fefefe80
> volume #2 color #fcfcfc80
> volume #2 color #fafafa80
> volume #2 color #f5f5f580
> volume #2 level 0.1057
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> dimers.png" width 1340 height 820 supersample 3
> select #1/o
7618 atoms, 7704 bonds, 2 pseudobonds, 463 residues, 2 models selected
> color (#!1 & sel) #aa0000ff
> select #1
74764 atoms, 75502 bonds, 50 pseudobonds, 4693 residues, 4 models selected
> ~select #1
Nothing selected
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> dimers.png" width 1340 height 820 supersample 3
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/Dimmers vs
> PolIRrn3.cxs"
> select rpa12++jaw++zincbindingribbon1
563 atoms, 566 bonds, 39 residues, 1 model selected
> select rpa12++linkerflexible
396 atoms, 398 bonds, 26 residues, 1 model selected
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> select rpa190++mimickingloop++tornero
Nothing selected
> select rpa190++funnel
2498 atoms, 2512 bonds, 165 residues, 1 model selected
> select rpa190++mimickingloop++tornero
Nothing selected
> select rpa190++activesite
1617 atoms, 1632 bonds, 104 residues, 1 model selected
> select #1/a:368-380
208 atoms, 209 bonds, 13 residues, 1 model selected
> hide #!1 models
> select #5/a:368-380
105 atoms, 106 bonds, 13 residues, 1 model selected
> view sel
> show #!1 models
> volume #2 level 0.09094
> select #1/a:368-380
208 atoms, 209 bonds, 13 residues, 1 model selected
> select sel :< 5
1453 atoms, 1456 bonds, 133 residues, 4 models selected
> select #1/a:368-380
208 atoms, 209 bonds, 13 residues, 1 model selected
> color #1/a:368-380 green
> color #1/a:368-380 map #2 green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color zone #2 near #1/a:368-380 distance 5
> color zone #2 near #1/a:368-380 distance 4
> color zone #2 near #1/a:368-380 distance 3
> volume #2 level 0.09304
> hide #!1 models
> color zone #2 near #1/a:368-380 distance 2
> color zone #2 near #1/a:368-380 distance 2.5
> volume #2 level 0.09515
> select #5/a:368-380
105 atoms, 106 bonds, 13 residues, 1 model selected
> view sel
> volume #2 level 0.08778
> color #5/a:368-380 green
> select #5
34302 atoms, 34772 bonds, 42 pseudobonds, 4491 residues, 3 models selected
> ~select #5
Nothing selected
> color zone #2 near #1/a:368-380 distance 22
> color zone #2 near #1/a:368-380 distance 22
> color zone #2 near #1/a:368-380 distance 2
> color zone #2 near #1/a:368-380 distance 2.5
> color zone #2 near #5/a:368-380 distance 1
> color zone #2 near #5/a:368-380 distance 0
> color zone #2 near #1/a:368-380 distance 1
> color zone #2 near #1/a:368-380 distance 1.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting soft
> lighting simple
> lighting full
> graphics silhouettes false
> lighting flat
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting soft
> lighting full
> lighting simple
> lighting simple
> lighting soft
> lighting simple
> lighting soft
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows false
> lighting flat
> lighting full
> lighting simple
> lighting soft
> lighting full
> view
> view
> volume #2 level 0.09936
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/Lid Loop.png"
> width 1340 height 819 supersample 3
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/lid.cxs"
> select rpa190++expander++engel
182 atoms, 181 bonds, 2 pseudobonds, 12 residues, 2 models selected
> view sel
> select #5/A:1337-1440
378 atoms, 379 bonds, 3 pseudobonds, 47 residues, 2 models selected
> view sel
> volume #2 level 0.1109
> color (#!5 & sel) #00aa00ff
> undo
> select #5/A:1360-1400
290 atoms, 292 bonds, 35 residues, 1 model selected
> view sel
> color sel #aa55ffff
> color sel #00aa00ff
> color sel #aa55ffff
> select #5/A:1337-1440
378 atoms, 379 bonds, 3 pseudobonds, 47 residues, 2 models selected
> color (#!5 & sel) #ff5500ff
> color (#!5 & sel) #aa55ffff
> color (#!5 & sel) #00aa00ff
> color (#!5 & sel) #00ffffff
> select #5/A:1360-1400
290 atoms, 292 bonds, 35 residues, 1 model selected
> color sel #00aa00ff
> color zone #2 near #1/a:368-380 distance 0
> select #5
34302 atoms, 34772 bonds, 42 pseudobonds, 4491 residues, 3 models selected
> ~select #5
Nothing selected
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/expander.png"
> width 1340 height 819 supersample 3
> volume #2 level 0.08567
> select #5/A:1337-1440
378 atoms, 379 bonds, 3 pseudobonds, 47 residues, 2 models selected
> select rpb12++zincribbon
549 atoms, 550 bonds, 34 residues, 1 model selected
> select rpb12
707 atoms, 708 bonds, 4 pseudobonds, 44 residues, 2 models selected
> select rpb12++zincribbon
549 atoms, 550 bonds, 34 residues, 1 model selected
> view sel
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> view sel
> hide rpa12++zincbindingribbon2 target c
> hide rpa12++zincbindingribbon2 target c
> hide rpa12++zincbindingribbon2 target c
> hide rpa12++zincbindingribbon2 target c
> color rpa12++zincbindingribbon2 #00aa00 target c
> show rpa12++linkerflexible target c
> show rpa12++linkerflexible target c
> show rpa12++linkerflexible target c
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!1 models
> view sel
> select rpa12
1640 atoms, 1649 bonds, 10 pseudobonds, 109 residues, 3 models selected
> view sel
> select #5/l
353 atoms, 354 bonds, 4 pseudobonds, 45 residues, 2 models selected
> hide #!1 models
> view sel
> select #5/l
353 atoms, 354 bonds, 4 pseudobonds, 45 residues, 2 models selected
> select #5/l
353 atoms, 354 bonds, 4 pseudobonds, 45 residues, 2 models selected
> show #!5 models
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> select rpa12++linkerflexible
396 atoms, 398 bonds, 26 residues, 1 model selected
> select rpa12++jaw++zincbindingribbon1
563 atoms, 566 bonds, 39 residues, 1 model selected
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> view sel
> hide #!2 models
> select #5/l
353 atoms, 354 bonds, 4 pseudobonds, 45 residues, 2 models selected
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> show rpa12++zincbindingribbon2 target c
> show rpa12++zincbindingribbon2 target c
> show rpa12++zincbindingribbon2 target c
> hide rpa12++zincbindingribbon2 target c
> select #1/L
707 atoms, 708 bonds, 4 pseudobonds, 44 residues, 2 models selected
> select #1/L
707 atoms, 708 bonds, 4 pseudobonds, 44 residues, 2 models selected
> select #1/L
707 atoms, 708 bonds, 4 pseudobonds, 44 residues, 2 models selected
> view sel
> show #!5 atoms
> hide #!5 atoms
> hide #!5 atoms
> hide #!5 cartoons
> select #5/l
353 atoms, 354 bonds, 4 pseudobonds, 45 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show sel atoms
> show #!2 models
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> select rpa12
1640 atoms, 1649 bonds, 10 pseudobonds, 109 residues, 3 models selected
> select rpa12
1640 atoms, 1649 bonds, 10 pseudobonds, 109 residues, 3 models selected
> hide #!5 cartoons
> hide #!5 cartoons
> show #!5 cartoons
> hide #!5 atoms
> select #5
34302 atoms, 34772 bonds, 42 pseudobonds, 4491 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> select #5/l
353 atoms, 354 bonds, 4 pseudobonds, 45 residues, 2 models selected
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> select rpa12++zincbindingribbon2
701 atoms, 705 bonds, 2 pseudobonds, 44 residues, 2 models selected
> select #5/l:65-125
53 atoms, 53 bonds, 6 residues, 1 model selected
> show sel cartoons
> open 4c2m
4c2m title:
Structure of RNA polymerase I at 2.8 A resolution [more info...]
Chain information for 4c2m #7
---
Chain | Description
1 L | DNA-directed RNA polymerases I, II, and III subunit rpabc 4
2 M | DNA-directed RNA polymerase I subunit RPA49
3 N | DNA-directed RNA polymerase I subunit RPA34
4 G O V | DNA-directed RNA polymerase I subunit RPA43
A P | DNA-directed RNA polymerase I subunit RPA190
B Q | DNA-directed RNA polymerase I subunit RPA135
C R | DNA-directed RNA polymerases I and III subunit RPAC1
D S | DNA-directed RNA polymerase I subunit RPA14
E T | DNA-directed RNA polymerases I, II, and III subunit rpabc 1
F U | DNA-directed RNA polymerases I, II, and III subunit rpabc 2
H W | DNA-directed RNA polymerases I, II, and III subunit rpabc 3
I X | DNA-directed RNA polymerase I subunit RPA12
J Y | DNA-directed RNA polymerases I, II, and III subunit rpabc 5
K Z | DNA-directed RNA polymerases I and III subunit RPAC2
Non-standard residues in 4c2m #7
---
SO4 — sulfate ion
ZN — zinc ion
4c2m mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> mmaker #7 to #5
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 4c2m_2_monomers.cif, chain A (#5) with 4c2m, chain A (#7), sequence
alignment score = 8342.4
RMSD between 1521 pruned atom pairs is 0.000 angstroms; (across all 1521
pairs: 0.000)
QWindowsWindow::setGeometry: Unable to set geometry 458x179+1570+510 (frame:
476x226+1561+472) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 575x226+1571+517 (frame:
593x273+1562+479) margins: 9, 38, 9, 9 minimum size: 89x1 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=107,48
maxtrack=524305,524334)
QWindowsWindow::setGeometry: Unable to set geometry 458x59+1595+422 (frame:
476x106+1586+384) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 575x76+1596+429 (frame:
593x123+1587+391) margins: 9, 38, 9, 9 minimum size: 89x1 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=107,48
maxtrack=524305,524334)
> select #7 i
Expected a keyword
> select #7/i
948 atoms, 956 bonds, 8 pseudobonds, 129 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #7
69107 atoms, 70162 bonds, 90 pseudobonds, 8943 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> select #7/i
948 atoms, 956 bonds, 8 pseudobonds, 129 residues, 2 models selected
> show sel cartoons
> show sel atoms
> view sel
> hide sel atoms
> hide sel cartoons
> select #5/i
948 atoms, 956 bonds, 8 pseudobonds, 129 residues, 2 models selected
> close #7
> hide #!5 models
> show #!5 models
> hide sel cartoons
> hide sel cartoons
> hide sel atoms
> select #5
34302 atoms, 34772 bonds, 42 pseudobonds, 4491 residues, 3 models selected
> hide sel cartoons
> select #5/i
948 atoms, 956 bonds, 8 pseudobonds, 129 residues, 2 models selected
> show sel cartoons
> volume #2 level 0.08364
> color (#!5 & sel) #00aa7fff
> color (#!5 & sel) #00aa00ff
> select #5
34302 atoms, 34772 bonds, 42 pseudobonds, 4491 residues, 3 models selected
> ~select #5
Nothing selected
> volume #2 level 0.08466
> show #!1 models
> select #1/i
1640 atoms, 1649 bonds, 10 pseudobonds, 109 residues, 3 models selected
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> volume #2 level 0.09276
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> lighting simple
> lighting full
> lighting soft
> lighting full
> lighting simple
> lighting flat
> lighting flat
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/A12.png" width
> 1340 height 819 supersample 3
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I
> Maps/Fig_PolIRrn3_Dimers.cxs"
> close #6
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/dim-
> cropped.mrc"
Opened dim-cropped.mrc, grid size 160,160,160, pixel 2.16, shown at level
0.085, step 1, values float32
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/mono-WT.mrc"
Opened mono-WT.mrc, grid size 128,128,128, pixel 2.16, shown at level 0.121,
step 1, values float32
> volume resample #6 onGrid #2
> close #6
> fitmap #8 inMap #2
Fit map dim-cropped.mrc resampled in map polI-Rrn3.mrc using 40872 points
correlation = 0.6007, correlation about mean = 0.08721, overlap = 294.1
steps = 328, shift = 105, angle = 17.4 degrees
Position of dim-cropped.mrc resampled (#8) relative to polI-Rrn3.mrc (#2)
coordinates:
Matrix rotation and translation
0.99917909 -0.02089462 0.03470666 -25.77575262
0.03024907 0.95467815 -0.29609901 -33.38513749
-0.02694681 0.29690578 0.95452649 -101.12361057
Axis 0.99099923 0.10303212 0.08546871
Axis point 0.00000000 307.29313455 -146.69249775
Rotation angle (degrees) 17.40928236
Shift along axis -37.62639739
> fitmap #8 inMap #2 search 50
Found 45 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (49 of 50).
Correlations and times found:
0.9432 (4), 0.6531 (1), 0.6528 (1), 0.6525 (1), 0.6522 (1), 0.6498 (1), 0.6466
(1), 0.6457 (1), 0.643 (1), 0.6419 (1), 0.6418 (1), 0.6415 (1), 0.641 (1),
0.6394 (1), 0.6385 (1), 0.6368 (1), 0.6336 (2), 0.6331 (1), 0.6326 (1), 0.6277
(1), 0.6232 (1), 0.6216 (1), 0.6187 (1), 0.6172 (1), 0.6157 (1), 0.6153 (1),
0.6128 (1), 0.6126 (1), 0.6109 (1), 0.6086 (1), 0.6084 (1), 0.6054 (1), 0.6014
(1), 0.5987 (1), 0.5971 (1), 0.5933 (1), 0.5861 (1), 0.5852 (1), 0.5844 (1),
0.5776 (1), 0.5199 (1), 0.4637 (1), 0.4557 (1), 0.3851 (1), 0.2997 (1)
Best fit found:
Fit map dim-cropped.mrc resampled in map polI-Rrn3.mrc using 40872 points
correlation = 0.9432, correlation about mean = 0.5812, overlap = 730.8
steps = 488, shift = 124, angle = 66.3 degrees
Position of dim-cropped.mrc resampled (#8) relative to polI-Rrn3.mrc (#2)
coordinates:
Matrix rotation and translation
-0.02850820 0.99116909 -0.12950293 -50.48995347
-0.01215797 0.12920216 0.99154371 -60.51774464
0.99951961 0.02984159 0.00836725 -42.70207283
Axis -0.53708543 -0.63052950 -0.56033186
Axis point -3.04668132 -0.00000000 4.27172028
Rotation angle (degrees) 116.45337447
Shift along axis 89.20297335
Found 45 fits. List window not yet implemented.
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/dim.mrc"
Opened dim.mrc, grid size 160,160,160, pixel 2.16, shown at level 0.132, step
1, values float32
> volume resample #6 onGrid #2
> close #6
> select #9
4 models selected
> fitmap #9 inMap #2 search 50
Found 49 unique fits from 50 random placements having fraction of points
inside contour >= 0.100 (50 of 50).
Correlations and times found:
0.6756 (2), 0.6252 (1), 0.4934 (1), 0.4808 (1), 0.4808 (1), 0.4804 (1), 0.4776
(1), 0.4772 (1), 0.4764 (1), 0.476 (1), 0.4748 (1), 0.4663 (1), 0.4582 (1),
0.4546 (1), 0.4539 (1), 0.4496 (1), 0.4488 (1), 0.4468 (1), 0.4457 (1), 0.4446
(1), 0.4413 (1), 0.4402 (1), 0.4357 (1), 0.4353 (1), 0.4352 (1), 0.4339 (1),
0.4334 (1), 0.4317 (1), 0.4316 (1), 0.4308 (1), 0.427 (1), 0.4258 (1), 0.4245
(1), 0.4194 (1), 0.4154 (1), 0.413 (1), 0.4109 (1), 0.4103 (1), 0.4091 (1),
0.4046 (1), 0.4018 (1), 0.4013 (1), 0.3977 (1), 0.3964 (1), 0.3949 (1), 0.393
(1), 0.3816 (1), 0.3106 (1), 0.3062 (1)
Best fit found:
Fit map dim.mrc resampled in map polI-Rrn3.mrc using 40922 points
correlation = 0.6756, correlation about mean = 0.1855, overlap = 589.2
steps = 516, shift = 70, angle = 68.7 degrees
Position of dim.mrc resampled (#9) relative to polI-Rrn3.mrc (#2) coordinates:
Matrix rotation and translation
-0.02524074 0.98792402 -0.15286915 -47.10873031
0.01158202 0.15319659 0.98812785 -71.54924189
0.99961430 0.02317052 -0.01530895 -37.85610618
Axis -0.53836830 -0.64299274 -0.54472003
Axis point 0.48501498 0.00000000 12.54463798
Rotation angle (degrees) 116.33869607
Shift along axis 91.98846942
Found 49 fits. List window not yet implemented.
> view sel
> view
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> Mono vs Dimers/PolIRrn3 Mono Dimer.cxs"
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!5 models
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> Mono vs Dimers/r3md.cxs"
opened ChimeraX session
QWindowsWindow::setGeometry: Unable to set geometry 458x169+1380+686 (frame:
476x216+1371+648) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 575x213+1381+693 (frame:
593x260+1372+655) margins: 9, 38, 9, 9 minimum size: 89x1 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=107,48
maxtrack=524305,524334)
QWindowsWindow::setGeometry: Unable to set geometry 458x103+1624+715 (frame:
476x150+1615+677) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 575x131+1625+722 (frame:
593x178+1616+684) margins: 9, 38, 9, 9 minimum size: 89x51 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=107,98
maxtrack=524305,524334)
> show #!7 models
> hide #!2 models
> hide #!7 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> hide #!8 models
> show #!8 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> volume #7 level 0.1195
> show #!2 models
> hide #!8 models
> volume #7 level 0.08599
> fitmap #7 inMap #2
Fit map mono-WT.mrc in map polI-Rrn3.mrc using 44562 points
correlation = 0.9568, correlation about mean = 0.6778, overlap = 746.1
steps = 72, shift = 3.28, angle = 4.37 degrees
Position of mono-WT.mrc (#7) relative to polI-Rrn3.mrc (#2) coordinates:
Matrix rotation and translation
0.99828592 -0.05660724 0.01486047 6.53093956
0.05581393 0.99722561 0.04925320 -17.39176198
-0.01760733 -0.04833936 0.99867577 8.93804927
Axis -0.64049213 0.21308357 0.73781111
Axis point 311.19968799 91.30487304 0.00000000
Rotation angle (degrees) 4.36934736
Shift along axis -1.29432203
> fitmap #8 inMap #2
Fit map dim-cropped.mrc resampled in map polI-Rrn3.mrc using 40872 points
correlation = 0.9431, correlation about mean = 0.581, overlap = 730.8
steps = 28, shift = 0.042, angle = 0.0169 degrees
Position of dim-cropped.mrc resampled (#8) relative to polI-Rrn3.mrc (#2)
coordinates:
Matrix rotation and translation
-0.02840782 0.99120281 -0.12926665 -50.59461919
-0.01201030 0.12897103 0.99157560 -60.51053056
0.99952425 0.02972100 0.00824082 -42.64345394
Axis -0.53720898 -0.63044520 -0.56030828
Axis point -3.12559150 0.00000000 4.25933179
Rotation angle (degrees) 116.46160418
Shift along axis 89.22193734
> volume #9 level 0.1338
> fitmap #9 inMap #2
Fit map dim.mrc resampled in map polI-Rrn3.mrc using 40047 points
correlation = 0.6763, correlation about mean = 0.1835, overlap = 582.9
steps = 148, shift = 0.041, angle = 0.0138 degrees
Position of dim.mrc resampled (#9) relative to polI-Rrn3.mrc (#2) coordinates:
Matrix rotation and translation
-0.02546660 0.98791520 -0.15288871 -47.08321967
0.01166049 0.15322145 0.98812307 -71.59287997
0.99960766 0.02338136 -0.01542162 -37.89681782
Axis -0.53829465 -0.64305567 -0.54471853
Axis point 0.52060027 0.00000000 12.55815161
Rotation angle (degrees) 116.34872319
Shift along axis 92.02595153
> show #!5 models
> hide #!5 models
> show #!4 models
> select #4
34286 atoms, 34758 bonds, 42 pseudobonds, 4488 residues, 3 models selected
> hide #5.1 models
> hide #5.2 models
> show #!7 models
> hide #!2 models
> ui tool show ISOLDE
> set selectionWidth 4
Done loading forcefield
> select #4/B:1170-1203
269 atoms, 273 bonds, 34 residues, 1 model selected
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/G ARG 241
CB because it is missing heavy-atom bond partners
Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/O LYS 57 CB because
it is missing heavy-atom bond partners
Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/O PHE 162 CB because
it is missing heavy-atom bond partners
Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/O ASN 210 CB because
it is missing heavy-atom bond partners
Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/O ASN 214 CB because
it is missing heavy-atom bond partners
1 messages similar to the above omitted
notes | Termini for 4c2m_2_monomers.cif (#5) chain A determined from SEQRES
records
Termini for 4c2m_2_monomers.cif (#5) chain B determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#5) chain C determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#5) chain D determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#5) chain E determined from SEQRES records
10 messages similar to the above omitted
Chain-initial residues that are actual N termini: 4c2m_2_monomers.cif #5/A MET
1, 4c2m_2_monomers.cif #5/J MET 1
Chain-initial residues that are not actual N termini: 4c2m_2_monomers.cif #5/A
SER 174, 4c2m_2_monomers.cif #5/A SER 312, 4c2m_2_monomers.cif #5/A ALA 1213,
4c2m_2_monomers.cif #5/A ALA 1286, 4c2m_2_monomers.cif #5/A PRO 1342,
4c2m_2_monomers.cif #5/A ASN 1361, 4c2m_2_monomers.cif #5/A ASN 1440,
4c2m_2_monomers.cif #5/B PRO 8, 4c2m_2_monomers.cif #5/B ASN 87,
4c2m_2_monomers.cif #5/B ILE 1151, 4c2m_2_monomers.cif #5/C TRP 31,
4c2m_2_monomers.cif #5/D THR 12, 4c2m_2_monomers.cif #5/D THR 80,
4c2m_2_monomers.cif #5/E GLU 4, 4c2m_2_monomers.cif #5/F PRO 55,
4c2m_2_monomers.cif #5/G ALA 14, 4c2m_2_monomers.cif #5/G GLY 215,
4c2m_2_monomers.cif #5/H ASN 3, 4c2m_2_monomers.cif #5/H SER 78,
4c2m_2_monomers.cif #5/I SER 2, 4c2m_2_monomers.cif #5/K PRO 42,
4c2m_2_monomers.cif #5/L LEU 27, 4c2m_2_monomers.cif #5/M SER 8,
4c2m_2_monomers.cif #5/N SER 24, 4c2m_2_monomers.cif #5/N LYS 49,
4c2m_2_monomers.cif #5/N THR 78, 4c2m_2_monomers.cif #5/O SER 265
Chain-final residues that are actual C termini: 4c2m_2_monomers.cif #5/A ALA
1664, 4c2m_2_monomers.cif #5/B LYS 1203, 4c2m_2_monomers.cif #5/C GLN 335,
4c2m_2_monomers.cif #5/E MET 215, 4c2m_2_monomers.cif #5/H ARG 146,
4c2m_2_monomers.cif #5/I ASN 125, 4c2m_2_monomers.cif #5/K MET 142,
4c2m_2_monomers.cif #5/L ARG 70
Chain-final residues that are not actual C termini: 4c2m_2_monomers.cif #5/A
LEU 141, 4c2m_2_monomers.cif #5/A ASP 273, 4c2m_2_monomers.cif #5/A PHE 1205,
4c2m_2_monomers.cif #5/A THR 1276, 4c2m_2_monomers.cif #5/A THR 1339,
4c2m_2_monomers.cif #5/A PRO 1349, 4c2m_2_monomers.cif #5/A MET 1395,
4c2m_2_monomers.cif #5/B SER 81, 4c2m_2_monomers.cif #5/B LEU 1141,
4c2m_2_monomers.cif #5/D GLU 48, 4c2m_2_monomers.cif #5/D PRO 100,
4c2m_2_monomers.cif #5/F ASP 154, 4c2m_2_monomers.cif #5/G HIS 170,
4c2m_2_monomers.cif #5/G ILE 250, 4c2m_2_monomers.cif #5/H ASN 64,
4c2m_2_monomers.cif #5/J ARG 69, 4c2m_2_monomers.cif #5/M SER 115,
4c2m_2_monomers.cif #5/N ASN 41, 4c2m_2_monomers.cif #5/N VAL 72,
4c2m_2_monomers.cif #5/N PHE 180, 4c2m_2_monomers.cif #5/O GLN 266
Missing OXT added to C-terminal residue 4c2m_2_monomers.cif #5/A ALA 1664
4509 hydrogen bonds
Adding 'H' to 4c2m_2_monomers.cif #5/A SER 174
Adding 'H' to 4c2m_2_monomers.cif #5/A SER 312
Adding 'H' to 4c2m_2_monomers.cif #5/A ALA 1213
Adding 'H' to 4c2m_2_monomers.cif #5/A ALA 1286
Adding 'H' to 4c2m_2_monomers.cif #5/A ASN 1361
18 messages similar to the above omitted
4c2m_2_monomers.cif #5/D PRO 100 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #5/F ASP 154 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #5/G ILE 250 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #5/J ARG 69 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #5/M SER 115 is not terminus, removing H atom from 'C'
2 messages similar to the above omitted
Termini for PolIRrn3fittes_complete.cif (#1.2) chain A determined from SEQRES
records
Termini for PolIRrn3fittes_complete.cif (#1.2) chain B determined from SEQRES
records
Termini for PolIRrn3fittes_complete.cif (#1.2) chain C determined from SEQRES
records
Termini for PolIRrn3fittes_complete.cif (#1.2) chain D determined from SEQRES
records
Termini for PolIRrn3fittes_complete.cif (#1.2) chain E determined from SEQRES
records
10 messages similar to the above omitted
Chain-initial residues that are actual N termini: PolIRrn3fittes_complete.cif
#1.2/A MET 1, PolIRrn3fittes_complete.cif #1.2/J MET 1
Chain-initial residues that are not actual N termini:
PolIRrn3fittes_complete.cif #1.2/A SER 174, PolIRrn3fittes_complete.cif #1.2/A
SER 312, PolIRrn3fittes_complete.cif #1.2/A SER 1016,
PolIRrn3fittes_complete.cif #1.2/A ALA 1213, PolIRrn3fittes_complete.cif
#1.2/A ALA 1286, PolIRrn3fittes_complete.cif #1.2/A PRO 1342,
PolIRrn3fittes_complete.cif #1.2/A ASN 1440, PolIRrn3fittes_complete.cif
#1.2/B THR 13, PolIRrn3fittes_complete.cif #1.2/B ASN 87,
PolIRrn3fittes_complete.cif #1.2/B ASP 1042, PolIRrn3fittes_complete.cif
#1.2/B ILE 1151, PolIRrn3fittes_complete.cif #1.2/C TRP 31,
PolIRrn3fittes_complete.cif #1.2/D THR 12, PolIRrn3fittes_complete.cif #1.2/D
THR 80, PolIRrn3fittes_complete.cif #1.2/E GLU 4, PolIRrn3fittes_complete.cif
#1.2/F PRO 55, PolIRrn3fittes_complete.cif #1.2/G ALA 14,
PolIRrn3fittes_complete.cif #1.2/G GLY 215, PolIRrn3fittes_complete.cif #1.2/H
ASN 3, PolIRrn3fittes_complete.cif #1.2/H SER 78, PolIRrn3fittes_complete.cif
#1.2/I SER 2, PolIRrn3fittes_complete.cif #1.2/I THR 81,
PolIRrn3fittes_complete.cif #1.2/I VAL 110, PolIRrn3fittes_complete.cif #1.2/K
PRO 42, PolIRrn3fittes_complete.cif #1.2/L LEU 27, PolIRrn3fittes_complete.cif
#1.2/M SER 8, PolIRrn3fittes_complete.cif #1.2/N SER 24,
PolIRrn3fittes_complete.cif #1.2/N LYS 49, PolIRrn3fittes_complete.cif #1.2/N
THR 78, PolIRrn3fittes_complete.cif #1.2/O SER 48, PolIRrn3fittes_complete.cif
#1.2/O GLY 324, PolIRrn3fittes_complete.cif #1.2/O THR 581
Chain-final residues that are actual C termini: PolIRrn3fittes_complete.cif
#1.2/B LYS 1203, PolIRrn3fittes_complete.cif #1.2/C GLN 335,
PolIRrn3fittes_complete.cif #1.2/E MET 215, PolIRrn3fittes_complete.cif #1.2/H
ARG 146, PolIRrn3fittes_complete.cif #1.2/I ASN 125,
PolIRrn3fittes_complete.cif #1.2/K MET 142
Chain-final residues that are not actual C termini:
PolIRrn3fittes_complete.cif #1.2/A LEU 141, PolIRrn3fittes_complete.cif #1.2/A
ASP 273, PolIRrn3fittes_complete.cif #1.2/A VAL 1011,
PolIRrn3fittes_complete.cif #1.2/A PHE 1205, PolIRrn3fittes_complete.cif
#1.2/A THR 1276, PolIRrn3fittes_complete.cif #1.2/A THR 1339,
PolIRrn3fittes_complete.cif #1.2/A PRO 1349, PolIRrn3fittes_complete.cif
#1.2/A ASN 1662, PolIRrn3fittes_complete.cif #1.2/B SER 81,
PolIRrn3fittes_complete.cif #1.2/B HIS 1038, PolIRrn3fittes_complete.cif
#1.2/B LEU 1141, PolIRrn3fittes_complete.cif #1.2/D GLU 48,
PolIRrn3fittes_complete.cif #1.2/D PRO 100, PolIRrn3fittes_complete.cif #1.2/F
ASP 154, PolIRrn3fittes_complete.cif #1.2/G HIS 170,
PolIRrn3fittes_complete.cif #1.2/G ILE 250, PolIRrn3fittes_complete.cif #1.2/H
ASN 64, PolIRrn3fittes_complete.cif #1.2/I ASN 74, PolIRrn3fittes_complete.cif
#1.2/I THR 98, PolIRrn3fittes_complete.cif #1.2/J ARG 69,
PolIRrn3fittes_complete.cif #1.2/L ALA 69, PolIRrn3fittes_complete.cif #1.2/M
LYS 112, PolIRrn3fittes_complete.cif #1.2/N ASN 41,
PolIRrn3fittes_complete.cif #1.2/N VAL 72, PolIRrn3fittes_complete.cif #1.2/N
PHE 180, PolIRrn3fittes_complete.cif #1.2/O LEU 248,
PolIRrn3fittes_complete.cif #1.2/O ARG 551, PolIRrn3fittes_complete.cif #1.2/O
SER 614
4181 hydrogen bonds
PolIRrn3fittes_complete.cif #1.2/A ASN 1662 is not terminus, removing H atom
from 'C'
PolIRrn3fittes_complete.cif #1.2/D PRO 100 is not terminus, removing H atom
from 'C'
PolIRrn3fittes_complete.cif #1.2/F ASP 154 is not terminus, removing H atom
from 'C'
PolIRrn3fittes_complete.cif #1.2/G ILE 250 is not terminus, removing H atom
from 'C'
PolIRrn3fittes_complete.cif #1.2/J ARG 69 is not terminus, removing H atom
from 'C'
4 messages similar to the above omitted
Termini for 4c2m_2_monomers.cif (#4.2) chain A determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#4.2) chain B determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#4.2) chain C determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#4.2) chain D determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#4.2) chain E determined from SEQRES records
9 messages similar to the above omitted
Chain-initial residues that are actual N termini: 4c2m_2_monomers.cif #4.2/A
MET 1, 4c2m_2_monomers.cif #4.2/J MET 1
Chain-initial residues that are not actual N termini: 4c2m_2_monomers.cif
#4.2/A SER 174, 4c2m_2_monomers.cif #4.2/A SER 312, 4c2m_2_monomers.cif #4.2/A
ALA 1213, 4c2m_2_monomers.cif #4.2/A ALA 1286, 4c2m_2_monomers.cif #4.2/A PRO
1342, 4c2m_2_monomers.cif #4.2/A ASN 1361, 4c2m_2_monomers.cif #4.2/A ASN
1440, 4c2m_2_monomers.cif #4.2/B PRO 8, 4c2m_2_monomers.cif #4.2/B ASN 87,
4c2m_2_monomers.cif #4.2/B ILE 1151, 4c2m_2_monomers.cif #4.2/C TRP 31,
4c2m_2_monomers.cif #4.2/D THR 12, 4c2m_2_monomers.cif #4.2/D THR 80,
4c2m_2_monomers.cif #4.2/E GLU 4, 4c2m_2_monomers.cif #4.2/F PRO 55,
4c2m_2_monomers.cif #4.2/G ALA 14, 4c2m_2_monomers.cif #4.2/G GLY 215,
4c2m_2_monomers.cif #4.2/H ASN 3, 4c2m_2_monomers.cif #4.2/H SER 78,
4c2m_2_monomers.cif #4.2/I SER 2, 4c2m_2_monomers.cif #4.2/K PRO 42,
4c2m_2_monomers.cif #4.2/L LEU 27, 4c2m_2_monomers.cif #4.2/M SER 8,
4c2m_2_monomers.cif #4.2/N SER 24, 4c2m_2_monomers.cif #4.2/N LYS 49,
4c2m_2_monomers.cif #4.2/N THR 78
Chain-final residues that are actual C termini: 4c2m_2_monomers.cif #4.2/A ALA
1664, 4c2m_2_monomers.cif #4.2/B LYS 1203, 4c2m_2_monomers.cif #4.2/C GLN 335,
4c2m_2_monomers.cif #4.2/E MET 215, 4c2m_2_monomers.cif #4.2/H ARG 146,
4c2m_2_monomers.cif #4.2/I ASN 125, 4c2m_2_monomers.cif #4.2/K MET 142,
4c2m_2_monomers.cif #4.2/L ARG 70
Chain-final residues that are not actual C termini: 4c2m_2_monomers.cif #4.2/A
LEU 141, 4c2m_2_monomers.cif #4.2/A ASP 273, 4c2m_2_monomers.cif #4.2/A PHE
1205, 4c2m_2_monomers.cif #4.2/A THR 1276, 4c2m_2_monomers.cif #4.2/A THR
1339, 4c2m_2_monomers.cif #4.2/A PRO 1349, 4c2m_2_monomers.cif #4.2/A MET
1395, 4c2m_2_monomers.cif #4.2/B SER 81, 4c2m_2_monomers.cif #4.2/B LEU 1141,
4c2m_2_monomers.cif #4.2/D GLU 48, 4c2m_2_monomers.cif #4.2/D PRO 100,
4c2m_2_monomers.cif #4.2/F ASP 154, 4c2m_2_monomers.cif #4.2/G HIS 170,
4c2m_2_monomers.cif #4.2/G ILE 250, 4c2m_2_monomers.cif #4.2/H ASN 64,
4c2m_2_monomers.cif #4.2/J ARG 69, 4c2m_2_monomers.cif #4.2/M SER 115,
4c2m_2_monomers.cif #4.2/N ASN 41, 4c2m_2_monomers.cif #4.2/N VAL 72,
4c2m_2_monomers.cif #4.2/N PHE 180
Missing OXT added to C-terminal residue 4c2m_2_monomers.cif #4.2/A ALA 1664
4506 hydrogen bonds
Adding 'H' to 4c2m_2_monomers.cif #4.2/A SER 174
Adding 'H' to 4c2m_2_monomers.cif #4.2/A SER 312
Adding 'H' to 4c2m_2_monomers.cif #4.2/A ALA 1213
Adding 'H' to 4c2m_2_monomers.cif #4.2/A ALA 1286
Adding 'H' to 4c2m_2_monomers.cif #4.2/A ASN 1361
17 messages similar to the above omitted
4c2m_2_monomers.cif #4.2/D PRO 100 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #4.2/F ASP 154 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #4.2/G ILE 250 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #4.2/J ARG 69 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #4.2/M SER 115 is not terminus, removing H atom from 'C'
1 messages similar to the above omitted
69056 hydrogens added
Loading residue template for SO4 from internal database
> addh
Summary of feedback from adding hydrogens to multiple structures
---
warnings | Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/G ARG 241
CB because it is missing heavy-atom bond partners
Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/O LYS 57 CB because
it is missing heavy-atom bond partners
Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/O PHE 162 CB because
it is missing heavy-atom bond partners
Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/O ASN 210 CB because
it is missing heavy-atom bond partners
Not adding hydrogens to PolIRrn3fittes_complete.cif #1.2/O ASN 214 CB because
it is missing heavy-atom bond partners
1 messages similar to the above omitted
notes | Termini for 4c2m_2_monomers.cif (#5) chain A determined from SEQRES
records
Termini for 4c2m_2_monomers.cif (#5) chain B determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#5) chain C determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#5) chain D determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#5) chain E determined from SEQRES records
10 messages similar to the above omitted
Chain-initial residues that are actual N termini: 4c2m_2_monomers.cif #5/A MET
1, 4c2m_2_monomers.cif #5/J MET 1
Chain-initial residues that are not actual N termini: 4c2m_2_monomers.cif #5/A
SER 174, 4c2m_2_monomers.cif #5/A SER 312, 4c2m_2_monomers.cif #5/A ALA 1213,
4c2m_2_monomers.cif #5/A ALA 1286, 4c2m_2_monomers.cif #5/A PRO 1342,
4c2m_2_monomers.cif #5/A ASN 1361, 4c2m_2_monomers.cif #5/A ASN 1440,
4c2m_2_monomers.cif #5/B PRO 8, 4c2m_2_monomers.cif #5/B ASN 87,
4c2m_2_monomers.cif #5/B ILE 1151, 4c2m_2_monomers.cif #5/C TRP 31,
4c2m_2_monomers.cif #5/D THR 12, 4c2m_2_monomers.cif #5/D THR 80,
4c2m_2_monomers.cif #5/E GLU 4, 4c2m_2_monomers.cif #5/F PRO 55,
4c2m_2_monomers.cif #5/G ALA 14, 4c2m_2_monomers.cif #5/G GLY 215,
4c2m_2_monomers.cif #5/H ASN 3, 4c2m_2_monomers.cif #5/H SER 78,
4c2m_2_monomers.cif #5/I SER 2, 4c2m_2_monomers.cif #5/K PRO 42,
4c2m_2_monomers.cif #5/L LEU 27, 4c2m_2_monomers.cif #5/M SER 8,
4c2m_2_monomers.cif #5/N SER 24, 4c2m_2_monomers.cif #5/N LYS 49,
4c2m_2_monomers.cif #5/N THR 78, 4c2m_2_monomers.cif #5/O SER 265
Chain-final residues that are actual C termini: 4c2m_2_monomers.cif #5/A ALA
1664, 4c2m_2_monomers.cif #5/B LYS 1203, 4c2m_2_monomers.cif #5/C GLN 335,
4c2m_2_monomers.cif #5/E MET 215, 4c2m_2_monomers.cif #5/H ARG 146,
4c2m_2_monomers.cif #5/I ASN 125, 4c2m_2_monomers.cif #5/K MET 142,
4c2m_2_monomers.cif #5/L ARG 70
Chain-final residues that are not actual C termini: 4c2m_2_monomers.cif #5/A
LEU 141, 4c2m_2_monomers.cif #5/A ASP 273, 4c2m_2_monomers.cif #5/A PHE 1205,
4c2m_2_monomers.cif #5/A THR 1276, 4c2m_2_monomers.cif #5/A THR 1339,
4c2m_2_monomers.cif #5/A PRO 1349, 4c2m_2_monomers.cif #5/A MET 1395,
4c2m_2_monomers.cif #5/B SER 81, 4c2m_2_monomers.cif #5/B LEU 1141,
4c2m_2_monomers.cif #5/D GLU 48, 4c2m_2_monomers.cif #5/D PRO 100,
4c2m_2_monomers.cif #5/F ASP 154, 4c2m_2_monomers.cif #5/G HIS 170,
4c2m_2_monomers.cif #5/G ILE 250, 4c2m_2_monomers.cif #5/H ASN 64,
4c2m_2_monomers.cif #5/J ARG 69, 4c2m_2_monomers.cif #5/M SER 115,
4c2m_2_monomers.cif #5/N ASN 41, 4c2m_2_monomers.cif #5/N VAL 72,
4c2m_2_monomers.cif #5/N PHE 180, 4c2m_2_monomers.cif #5/O GLN 266
4183 hydrogen bonds
4c2m_2_monomers.cif #5/D PRO 100 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #5/F ASP 154 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #5/G ILE 250 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #5/J ARG 69 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #5/M SER 115 is not terminus, removing H atom from 'C'
2 messages similar to the above omitted
Termini for PolIRrn3fittes_complete.cif (#1.2) chain A determined from SEQRES
records
Termini for PolIRrn3fittes_complete.cif (#1.2) chain B determined from SEQRES
records
Termini for PolIRrn3fittes_complete.cif (#1.2) chain C determined from SEQRES
records
Termini for PolIRrn3fittes_complete.cif (#1.2) chain D determined from SEQRES
records
Termini for PolIRrn3fittes_complete.cif (#1.2) chain E determined from SEQRES
records
10 messages similar to the above omitted
Chain-initial residues that are actual N termini: PolIRrn3fittes_complete.cif
#1.2/A MET 1, PolIRrn3fittes_complete.cif #1.2/J MET 1
Chain-initial residues that are not actual N termini:
PolIRrn3fittes_complete.cif #1.2/A SER 174, PolIRrn3fittes_complete.cif #1.2/A
SER 312, PolIRrn3fittes_complete.cif #1.2/A SER 1016,
PolIRrn3fittes_complete.cif #1.2/A ALA 1213, PolIRrn3fittes_complete.cif
#1.2/A ALA 1286, PolIRrn3fittes_complete.cif #1.2/A PRO 1342,
PolIRrn3fittes_complete.cif #1.2/A ASN 1440, PolIRrn3fittes_complete.cif
#1.2/B THR 13, PolIRrn3fittes_complete.cif #1.2/B ASN 87,
PolIRrn3fittes_complete.cif #1.2/B ASP 1042, PolIRrn3fittes_complete.cif
#1.2/B ILE 1151, PolIRrn3fittes_complete.cif #1.2/C TRP 31,
PolIRrn3fittes_complete.cif #1.2/D THR 12, PolIRrn3fittes_complete.cif #1.2/D
THR 80, PolIRrn3fittes_complete.cif #1.2/E GLU 4, PolIRrn3fittes_complete.cif
#1.2/F PRO 55, PolIRrn3fittes_complete.cif #1.2/G ALA 14,
PolIRrn3fittes_complete.cif #1.2/G GLY 215, PolIRrn3fittes_complete.cif #1.2/H
ASN 3, PolIRrn3fittes_complete.cif #1.2/H SER 78, PolIRrn3fittes_complete.cif
#1.2/I SER 2, PolIRrn3fittes_complete.cif #1.2/I THR 81,
PolIRrn3fittes_complete.cif #1.2/I VAL 110, PolIRrn3fittes_complete.cif #1.2/K
PRO 42, PolIRrn3fittes_complete.cif #1.2/L LEU 27, PolIRrn3fittes_complete.cif
#1.2/M SER 8, PolIRrn3fittes_complete.cif #1.2/N SER 24,
PolIRrn3fittes_complete.cif #1.2/N LYS 49, PolIRrn3fittes_complete.cif #1.2/N
THR 78, PolIRrn3fittes_complete.cif #1.2/O SER 48, PolIRrn3fittes_complete.cif
#1.2/O GLY 324, PolIRrn3fittes_complete.cif #1.2/O THR 581
Chain-final residues that are actual C termini: PolIRrn3fittes_complete.cif
#1.2/B LYS 1203, PolIRrn3fittes_complete.cif #1.2/C GLN 335,
PolIRrn3fittes_complete.cif #1.2/E MET 215, PolIRrn3fittes_complete.cif #1.2/H
ARG 146, PolIRrn3fittes_complete.cif #1.2/I ASN 125,
PolIRrn3fittes_complete.cif #1.2/K MET 142
Chain-final residues that are not actual C termini:
PolIRrn3fittes_complete.cif #1.2/A LEU 141, PolIRrn3fittes_complete.cif #1.2/A
ASP 273, PolIRrn3fittes_complete.cif #1.2/A VAL 1011,
PolIRrn3fittes_complete.cif #1.2/A PHE 1205, PolIRrn3fittes_complete.cif
#1.2/A THR 1276, PolIRrn3fittes_complete.cif #1.2/A THR 1339,
PolIRrn3fittes_complete.cif #1.2/A PRO 1349, PolIRrn3fittes_complete.cif
#1.2/A ASN 1662, PolIRrn3fittes_complete.cif #1.2/B SER 81,
PolIRrn3fittes_complete.cif #1.2/B HIS 1038, PolIRrn3fittes_complete.cif
#1.2/B LEU 1141, PolIRrn3fittes_complete.cif #1.2/D GLU 48,
PolIRrn3fittes_complete.cif #1.2/D PRO 100, PolIRrn3fittes_complete.cif #1.2/F
ASP 154, PolIRrn3fittes_complete.cif #1.2/G HIS 170,
PolIRrn3fittes_complete.cif #1.2/G ILE 250, PolIRrn3fittes_complete.cif #1.2/H
ASN 64, PolIRrn3fittes_complete.cif #1.2/I ASN 74, PolIRrn3fittes_complete.cif
#1.2/I THR 98, PolIRrn3fittes_complete.cif #1.2/J ARG 69,
PolIRrn3fittes_complete.cif #1.2/L ALA 69, PolIRrn3fittes_complete.cif #1.2/M
LYS 112, PolIRrn3fittes_complete.cif #1.2/N ASN 41,
PolIRrn3fittes_complete.cif #1.2/N VAL 72, PolIRrn3fittes_complete.cif #1.2/N
PHE 180, PolIRrn3fittes_complete.cif #1.2/O LEU 248,
PolIRrn3fittes_complete.cif #1.2/O ARG 551, PolIRrn3fittes_complete.cif #1.2/O
SER 614
4179 hydrogen bonds
PolIRrn3fittes_complete.cif #1.2/A ASN 1662 is not terminus, removing H atom
from 'C'
PolIRrn3fittes_complete.cif #1.2/D PRO 100 is not terminus, removing H atom
from 'C'
PolIRrn3fittes_complete.cif #1.2/F ASP 154 is not terminus, removing H atom
from 'C'
PolIRrn3fittes_complete.cif #1.2/G ILE 250 is not terminus, removing H atom
from 'C'
PolIRrn3fittes_complete.cif #1.2/J ARG 69 is not terminus, removing H atom
from 'C'
4 messages similar to the above omitted
Termini for 4c2m_2_monomers.cif (#4.2) chain A determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#4.2) chain B determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#4.2) chain C determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#4.2) chain D determined from SEQRES records
Termini for 4c2m_2_monomers.cif (#4.2) chain E determined from SEQRES records
9 messages similar to the above omitted
Chain-initial residues that are actual N termini: 4c2m_2_monomers.cif #4.2/A
MET 1, 4c2m_2_monomers.cif #4.2/J MET 1
Chain-initial residues that are not actual N termini: 4c2m_2_monomers.cif
#4.2/A SER 174, 4c2m_2_monomers.cif #4.2/A SER 312, 4c2m_2_monomers.cif #4.2/A
ALA 1213, 4c2m_2_monomers.cif #4.2/A ALA 1286, 4c2m_2_monomers.cif #4.2/A PRO
1342, 4c2m_2_monomers.cif #4.2/A ASN 1361, 4c2m_2_monomers.cif #4.2/A ASN
1440, 4c2m_2_monomers.cif #4.2/B PRO 8, 4c2m_2_monomers.cif #4.2/B ASN 87,
4c2m_2_monomers.cif #4.2/B ILE 1151, 4c2m_2_monomers.cif #4.2/C TRP 31,
4c2m_2_monomers.cif #4.2/D THR 12, 4c2m_2_monomers.cif #4.2/D THR 80,
4c2m_2_monomers.cif #4.2/E GLU 4, 4c2m_2_monomers.cif #4.2/F PRO 55,
4c2m_2_monomers.cif #4.2/G ALA 14, 4c2m_2_monomers.cif #4.2/G GLY 215,
4c2m_2_monomers.cif #4.2/H ASN 3, 4c2m_2_monomers.cif #4.2/H SER 78,
4c2m_2_monomers.cif #4.2/I SER 2, 4c2m_2_monomers.cif #4.2/K PRO 42,
4c2m_2_monomers.cif #4.2/L LEU 27, 4c2m_2_monomers.cif #4.2/M SER 8,
4c2m_2_monomers.cif #4.2/N SER 24, 4c2m_2_monomers.cif #4.2/N LYS 49,
4c2m_2_monomers.cif #4.2/N THR 78
Chain-final residues that are actual C termini: 4c2m_2_monomers.cif #4.2/A ALA
1664, 4c2m_2_monomers.cif #4.2/B LYS 1203, 4c2m_2_monomers.cif #4.2/C GLN 335,
4c2m_2_monomers.cif #4.2/E MET 215, 4c2m_2_monomers.cif #4.2/H ARG 146,
4c2m_2_monomers.cif #4.2/I ASN 125, 4c2m_2_monomers.cif #4.2/K MET 142,
4c2m_2_monomers.cif #4.2/L ARG 70
Chain-final residues that are not actual C termini: 4c2m_2_monomers.cif #4.2/A
LEU 141, 4c2m_2_monomers.cif #4.2/A ASP 273, 4c2m_2_monomers.cif #4.2/A PHE
1205, 4c2m_2_monomers.cif #4.2/A THR 1276, 4c2m_2_monomers.cif #4.2/A THR
1339, 4c2m_2_monomers.cif #4.2/A PRO 1349, 4c2m_2_monomers.cif #4.2/A MET
1395, 4c2m_2_monomers.cif #4.2/B SER 81, 4c2m_2_monomers.cif #4.2/B LEU 1141,
4c2m_2_monomers.cif #4.2/D GLU 48, 4c2m_2_monomers.cif #4.2/D PRO 100,
4c2m_2_monomers.cif #4.2/F ASP 154, 4c2m_2_monomers.cif #4.2/G HIS 170,
4c2m_2_monomers.cif #4.2/G ILE 250, 4c2m_2_monomers.cif #4.2/H ASN 64,
4c2m_2_monomers.cif #4.2/J ARG 69, 4c2m_2_monomers.cif #4.2/M SER 115,
4c2m_2_monomers.cif #4.2/N ASN 41, 4c2m_2_monomers.cif #4.2/N VAL 72,
4c2m_2_monomers.cif #4.2/N PHE 180
4175 hydrogen bonds
4c2m_2_monomers.cif #4.2/D PRO 100 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #4.2/F ASP 154 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #4.2/G ILE 250 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #4.2/J ARG 69 is not terminus, removing H atom from 'C'
4c2m_2_monomers.cif #4.2/M SER 115 is not terminus, removing H atom from 'C'
1 messages similar to the above omitted
0 hydrogens added
> select a++stalk
3974 atoms, 4018 bonds, 2 pseudobonds, 251 residues, 2 models selected
> select #1/D #1/G
3974 atoms, 4018 bonds, 2 pseudobonds, 251 residues, 2 models selected
> select #4/D #4/G
4003 atoms, 4043 bonds, 2 pseudobonds, 255 residues, 2 models selected
> volume #4.1.1.1 level 0.03787
> select 41/A:01-90 #4/A:350-477 #4/A:1608-1664
Expected an objects specifier or a keyword
> select #4/A:01-90 #4/A:350-477 #4/A:1608-1664
4304 atoms, 4338 bonds, 275 residues, 1 model selected
> volume #4.1.1.1 level 0.04104
> select #4
68806 atoms, 69278 bonds, 42 pseudobonds, 4488 residues, 20 models selected
> select #4
68806 atoms, 69278 bonds, 42 pseudobonds, 4488 residues, 20 models selected
> select #4
68806 atoms, 69278 bonds, 42 pseudobonds, 4488 residues, 20 models selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> volume #4.1.1.1 level 0.06039
> select #4/A:01-90 #4/A:350-477 #4/A:1608-1664
4304 atoms, 4338 bonds, 275 residues, 1 model selected
> select #4/a:368-380
208 atoms, 209 bonds, 13 residues, 1 model selected
> volume #4.1.1.1 level 0.1046
> hide #!1 models
> hide #1.1 models
> hide #1.3 models
> hide #4.3 models
> show #4.3 models
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> volume #4.1.1.1 style surface style image maximumIntensityProjection True
Repeated keyword argument "style"
> volume #4.1.1.1 style surface maximumIntensityProjection false
> volume #4.1.1.1 change image level 0.0256,0 level 0.1755,0.8 level 0.1884,1
> show #!1.2 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5
68837 atoms, 69307 bonds, 42 pseudobonds, 4491 residues, 3 models selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select #4
68806 atoms, 69278 bonds, 42 pseudobonds, 4488 residues, 21 models selected
> hide sel atoms
> show sel cartoons
> select #1
74767 atoms, 75505 bonds, 50 pseudobonds, 4693 residues, 11 models selected
> hide sel atoms
> show sel cartoons
> hide #!4.1 models
> show #!4.1 models
> hide #!4.1 models
> show #!4.1 models
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> Mono vs Dimers/r3md_v2.cxs"
opened ChimeraX session
QWindowsWindow::setGeometry: Unable to set geometry 458x197+1614+686 (frame:
476x244+1605+648) on QWidgetWindow/"QDockWidgetClassWindow" on
"\\\\.\DISPLAY2". Resulting geometry: 575x248+1615+693 (frame:
593x295+1606+655) margins: 9, 38, 9, 9 minimum size: 89x51 maximum size:
524287x524287 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=107,98
maxtrack=524305,524334)
> ui tool show ISOLDE
> set selectionWidth 4
Done loading forcefield
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.2 models
> hide #1.3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #3.1 models
> hide #!3 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #4.3 models
> hide #!4.2 models
> hide #!4.1 models
> hide #!4 models
> hide #!2 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> view
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> hide #!4.2 models
> show #!4.2 models
> show #!4.1 models
> volume #4.1.1.1 level 0.1355
> hide #!4.1.1 models
> show #!4.1.1 models
> hide #!4.1.1 models
> show #!4.1.1 models
> hide #!4.1 models
> show #!4.1 models
> show #!1.2 models
> show #!8 models
> show #!9 models
> close #4
> close #1
> close #3
> show #!2 models
> hide #!2 models
> show #!2 models
> save "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> Mono vs Dimers/IsoldeCLosed.cxs" includeMaps true
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/mono-WT.mrc"
Opened mono-WT.mrc, grid size 128,128,128, pixel 2.16, shown at level 0.121,
step 1, values float32
> hide #!9 models
> hide #!8 models
> hide #!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
> hide #!2 models
> show #!2 models
> hide #!2 models
> close session
> open "C:/Users/LocalAdmin/Desktop/Test ChimeraX/3DWS/rtuuu.cxs"
restore_snapshot for "RotamerRestraintMgr" returned None
restore_snapshot for "NXmapHandler" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 683, in restore
obj = sm.restore_snapshot(self, data)
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\molobject.py", line 2075, in restore_snapshot
auto_add_to_session=False)
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\molobject.py", line 1891, in __init__
name = 'MDFF - ' + volume.name
AttributeError: 'NoneType' object has no attribute 'name'
Exception ignored in: <function Drawing.__del__ at 0x000001D72F5A9A68>
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1170, in __del__
if not self.was_deleted:
AttributeError: 'MDFFMgr' object has no attribute 'was_deleted'
opened ChimeraX session
> open "C:/Users/LocalAdmin/Desktop/Test
> ChimeraX/3DWS/PolIRrn3MonoDim_1203.cxs"
restore_snapshot for "RotamerRestraintMgr" returned None
restore_snapshot for "NXmapHandler" returned None
Unable to restore session, resetting.
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 683, in restore
obj = sm.restore_snapshot(self, data)
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\molobject.py", line 2075, in restore_snapshot
auto_add_to_session=False)
File "C:\Users\LocalAdmin\AppData\Local\UCSF\ChimeraX\1.1\site-
packages\chimerax\isolde\molobject.py", line 1891, in __init__
name = 'MDFF - ' + volume.name
AttributeError: 'NoneType' object has no attribute 'name'
Exception ignored in: <function Drawing.__del__ at 0x000001D72F5A9A68>
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1170, in __del__
if not self.was_deleted:
AttributeError: 'MDFFMgr' object has no attribute 'was_deleted'
opened ChimeraX session
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> Mono vs Dimers/KeyElementsv2.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 608, in restore
version = serialize.pickle_deserialize(stream)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\serialize.py", line 57, in pickle_deserialize
return unpickler.load()
_pickle.UnpicklingError: invalid load key, '\x04'.
_pickle.UnpicklingError: invalid load key, '\x04'.
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\serialize.py", line 57, in pickle_deserialize
return unpickler.load()
See log for complete Python traceback.
> open "C:/Users/LocalAdmin/Desktop/These/Pol IRrn3/Pol I Maps/PolIRrn3 vs
> Mono vs Dimers/KeyElements.cxs"
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 150, in _qt_safe
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run
results = command.run(text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 100, in cmd_open
return Command(session, registry=registry).run(provider_cmd_text, log=log)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run
result = ci.function(session, **kw_args)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 154, in provider_open
name or model_name_from_path(fi.file_name)), provider_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 390, in collated_open
return func(*func_args, **func_kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 26, in open
return cxs_open(session, data, **kw)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 925, in open
session.restore(stream, path=path, resize_window=resize_window)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\session.py", line 608, in restore
version = serialize.pickle_deserialize(stream)
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\serialize.py", line 57, in pickle_deserialize
return unpickler.load()
_pickle.UnpicklingError: invalid load key, '\x04'.
_pickle.UnpicklingError: invalid load key, '\x04'.
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\serialize.py", line 57, in pickle_deserialize
return unpickler.load()
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 23.20.16.4973
OpenGL renderer: Intel(R) UHD Graphics 620
OpenGL vendor: Intel
Manufacturer: HP
Model: HP EliteBook 850 G5
OS: Microsoft Windows 10 Education (Build 18363)
Memory: 8,425,529,344
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.8.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.6.20
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.6.1
ChimeraX-AtomSearch: 2.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.0.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.0
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.0
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.1
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.0
ChimeraX-Help: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.0
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-ISOLDE: 1.1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.0
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.0
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.2.1
ChimeraX-PDB: 2.1
ChimeraX-PDBBio: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0
ChimeraX-PubChem: 2.0
ChimeraX-Read-Pbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.0
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.2
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.0.4
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.3
ChimeraX-uniprot: 2.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.20
decorator: 4.4.2
distlib: 0.3.1
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
gdcm: 2.8.8
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.16
imagecodecs: 2020.5.30
imagecodecs-lite: 2020.1.31
imagesize: 1.2.0
ipykernel: 5.3.0
ipython: 7.15.0
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.3
jupyter-core: 4.6.3
kiwisolver: 1.2.0
line-profiler: 2.1.2
lxml: 4.5.1
MarkupSafe: 1.1.1
matplotlib: 3.2.1
msgpack: 1.0.0
netifaces: 0.10.9
networkx: 2.4
numexpr: 2.7.1
numpy: 1.18.5+mkl
numpydoc: 1.0.0
openvr: 1.12.501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.1.2
pip: 20.2.2
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.7
psutil: 5.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.6.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.12.3
PyQt5-sip: 4.19.19
PyQtWebEngine-commercial: 5.12.1
python-dateutil: 2.8.1
pytz: 2020.1
pywin32: 228
pyzmq: 19.0.2
qtconsole: 4.7.4
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.4.1
setuptools: 49.4.0
sfftk-rw: 0.6.6.dev0
six: 1.15.0
snowballstemmer: 2.0.0
sortedcontainers: 2.2.2
Sphinx: 3.1.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.6.3
tinyarray: 1.2.2
tornado: 6.0.4
traitlets: 5.0.4
urllib3: 1.25.10
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.34.2
WMI: 1.5.1
Change History (1)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Session restore: _pickle.UnpicklingError: invalid load key |
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