Possibly fetching 'residues' of dead Structure

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/ISOLDE files/Final/Fixing clashes_final_J55-phenix-
> autosharpenmap_coot-itr6_rsr-18.cxs"

restore_snapshot for "RotamerRestraintMgr" returned None  

Opened J55_iteration9_no overall_sharpened_map.ccp4 as #1, grid size
250,250,250, pixel 1.07, shown at level 6.01, step 1, values float32  
Restoring stepper: J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb  
Log from Thu Jul 29 16:49:45 2021UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12
> 2020/Maps/Phenix/Job55/without model/No overall before/J55_iteration9_no
> overall_sharpened_map.ccp4"

Opened J55_iteration9_no overall_sharpened_map.ccp4 as #1, grid size
250,250,250, pixel 1.07, shown at level 3.95, step 1, values float32  

> set bgColor white

> surface dust #1 size 10.7

> volume #1 level 5.495

> volume #1 level 5.852

> volume #1 level 6.031

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Maps/3D
> refinements/Job55_NU refinement_BETA/Job70_local resolution
> estimation/cryosparc_P155_J70_map_locres.mrc"

Opened cryosparc_P155_J70_map_locres.mrc as #2, grid size 250,250,250, pixel
1.07, shown at level 5.6, step 1, values float32  

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> hide #!2 models

> color sample #1.1 map #2 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette #000000:#3f3f3f:#7f7f7f:#bfbfbf:#ffffff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette #0fc6ce:#87e2e6:#ffffff:#ce8fae:#9e1f5e

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette #ff0000:#ffff00:#00ff00

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette #ff0000:#ffff00:#00ff00:#00ffff:#0000ff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette
> 2,#ff0000:2.5,#ffff00:3,#00ff00:3.5,#00ffff:4,#0000ff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette
> 2.5,#ff0000:3,#ffff00:3.5,#00ff00:4,#00ffff:4.5,#0000ff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> color sample #1.1 map #2 palette
> 2.5,#ff0000:3,#ffff00:3.5,#00ff00:4,#00ffff:4.5,#0000ff

Map values for surface "surface": minimum 2.457, mean 2.751, maximum 6.889  

> key red:2.5 yellow:3.0 lime:3.5 cyan:4.0 blue:4.5

> ui tool show "Color Key"

> ui mousemode left "color key"

> key pos 0.874765,0.0942931 size 0,0

> ui mousemode left rotate

> key red:2.5 yellow:3.0 lime:3.5 cyan:4.0 blue:4.5

> ui tool show "Color Key"

> ui mousemode left "color key"

> key labelSide left/top

> key labelSide right/bottom

> key pos 0.862413,0.176032 size 0,0

> key pos 0.814152,0.170967 size 0.0543952,0.021249

> key pos 0.681495,0.181509 size 0.139542,0.0181042

> key pos 0.77342,0.154552 size 0.00686919,0.0357726

> key pos 0.661919,0.170803 size 0.123925,0.00123458

> key pos 0.706933,0.173891 size 0.00124881,0.0422907

> key pos 0.670494,0.122206 size 0.184106,0.0320224

> key pos 0.714991,0.117831 size 0.289452,0.0227895

Key is partially or completely offscreen  

> key pos 0.344989,0.03169

> key pos 0.327731,0.0837577

> lighting soft

> key pos 0.312527,0.0875446

> key pos 0,0.0928796 size 0.312966,0.037714

> key pos 0.0940082,0.0918544 size 0.453409,0.0124739

> key pos 0.224729,0.0994224

> key pos 0.224867,0.0867198 size 0.464295,0.0333742

> key bold true

> ui mousemode left rotate

> save /Users/yogesh/Desktop/image1.png supersample 3

> ui tool show "Side View"

> view orient

> save /Users/yogesh/Desktop/image1.png supersample 3

> view orient

> view orient

> view orient

> view orient

> view orient

> view

> view

> ui tool show "Side View"

> view orient

> view orient

> ui tool show "Side View"

> save /Users/yogesh/Desktop/image1.png supersample 3

> save "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Maps/3D
> refinements/Job55_NU refinement_BETA/Job70_local resolution
> estimation/figures_locres_J55_chimeraX.aln"

No alignments open!  

> close session

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Maps/3D
> refinements/Job55_NU refinement_BETA/cryosparc_P155_J55_009_volume_map.mrc"

Opened cryosparc_P155_J55_009_volume_map.mrc as #1, grid size 250,250,250,
pixel 1.07, shown at level 0.305, step 1, values float32  

> lighting soft

> lighting soft

> lighting simple

> lighting soft

> surface dust #1 size 10.7

> volume #1 level 0.3622

> volume #1 level 0.4058

> volume #1 level 0.4058

> volume #1 level 0.4527

> lighting full

> lighting soft

> lighting full

> lighting soft

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12
> 2020/Maps/Phenix/Job55/without model/No overall before/J55_iteration9_no
> overall_sharpened_map.ccp4"

Opened J55_iteration9_no overall_sharpened_map.ccp4 as #2, grid size
250,250,250, pixel 1.07, shown at level 3.95, step 1, values float32  

> surface dust #2 size 10.7

> volume #2 level 6.009

> volume #1 color #b3b3b3

> volume #2 color #fafafa

> volume #2 color #b3b3b3

> save /Users/yogesh/Desktop/image1.png supersample 3

> save /Users/yogesh/Desktop/image1.png supersample 3

> close session

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/J76-map_model-build-
> try1.py"

Traceback (most recent call last):  
File "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
building/Chimera files/Job76-map_model-building-try1/J76-map_model-build-
try1.py", line 1, in <module>  
import cPickle, base64  
ModuleNotFoundError: No module named 'cPickle'  
  
Error opening python file
/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
building/Chimera files/Job76-map_model-building-try1/J76-map_model-build-
try1.py  

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12
> 2020/Maps/Phenix/Job76/Without model/No overall before/J76_iteration8_no-
> overall_sharpened_map.ccp4"

Opened J76_iteration8_no-overall_sharpened_map.ccp4 as #1, grid size
250,250,250, pixel 1.07, shown at level 3.98, step 1, values float32  

> lighting soft

> lighting simple

> lighting soft

> surface dust #1 size 10.7

> volume #1 level 6.011

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-A.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-B.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-C.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-D.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-E.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscS-A.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscS-B.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscS-C.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscS-D.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscT-A.pdb"
> "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/Job76-map_EscU_n-
> term.pdb"

Summary of feedback from opening
/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-A.pdb  
---  
warnings | Ignored bad PDB record found on line 12  
METHOD  
  
Ignored bad PDB record found on line 13  
METHOD The models are generated by I-TASSER which combines the  
  
Ignored bad PDB record found on line 14  
METHOD methods of threading, ab initio modeling and structural  
  
Ignored bad PDB record found on line 15  
METHOD refinement. The procedure is fully automated.  
  
Ignored bad PDB record found on line 16  
METHOD  
  
7 messages similar to the above omitted  
  
Summary of feedback from opening
/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-B.pdb  
---  
warnings | Ignored bad PDB record found on line 12  
METHOD  
  
Ignored bad PDB record found on line 13  
METHOD The models are generated by I-TASSER which combines the  
  
Ignored bad PDB record found on line 14  
METHOD methods of threading, ab initio modeling and structural  
  
Ignored bad PDB record found on line 15  
METHOD refinement. The procedure is fully automated.  
  
Ignored bad PDB record found on line 16  
METHOD  
  
7 messages similar to the above omitted  
  
Summary of feedback from opening
/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-C.pdb  
---  
warnings | Ignored bad PDB record found on line 12  
METHOD  
  
Ignored bad PDB record found on line 13  
METHOD The models are generated by I-TASSER which combines the  
  
Ignored bad PDB record found on line 14  
METHOD methods of threading, ab initio modeling and structural  
  
Ignored bad PDB record found on line 15  
METHOD refinement. The procedure is fully automated.  
  
Ignored bad PDB record found on line 16  
METHOD  
  
7 messages similar to the above omitted  
  
Summary of feedback from opening
/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-D.pdb  
---  
warnings | Ignored bad PDB record found on line 12  
METHOD  
  
Ignored bad PDB record found on line 13  
METHOD The models are generated by I-TASSER which combines the  
  
Ignored bad PDB record found on line 14  
METHOD methods of threading, ab initio modeling and structural  
  
Ignored bad PDB record found on line 15  
METHOD refinement. The procedure is fully automated.  
  
Ignored bad PDB record found on line 16  
METHOD  
  
7 messages similar to the above omitted  
  
Summary of feedback from opening
/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
building/Chimera files/Job76-map_model-building-try1/Job76-map_EscR-E.pdb  
---  
warnings | Ignored bad PDB record found on line 12  
METHOD  
  
Ignored bad PDB record found on line 13  
METHOD The models are generated by I-TASSER which combines the  
  
Ignored bad PDB record found on line 14  
METHOD methods of threading, ab initio modeling and structural  
  
Ignored bad PDB record found on line 15  
METHOD refinement. The procedure is fully automated.  
  
Ignored bad PDB record found on line 16  
METHOD  
  
7 messages similar to the above omitted  
  
Chain information for Job76-map_EscR-A.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscR-B.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscR-C.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscR-D.pdb #5  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscR-E.pdb #6  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscS-A.pdb #7  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscS-B.pdb #8  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscS-C.pdb #9  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscS-D.pdb #10  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscT-A.pdb #11  
---  
Chain | Description  
A | No description available  
  
Chain information for Job76-map_EscU_n-term.pdb #12  
---  
Chain | Description  
? | No description available  
  

> save /Users/yogesh/Desktop/image1.png supersample 3

> save "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/Chimera files/Job76-map_model-building-try1/J76-map_model-build-
> try-1.cxs" includeMaps true

> close session

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12
> 2020/Maps/DeepEMhancer/From
> Yogesh/deppEMhancer_J55-Cryosparc/J55_009_highRes.mrc"

Opened J55_009_highRes.mrc as #1, grid size 250,250,250, pixel 1.07, shown at
level 0.00709, step 1, values float32  

> lighting soft

> lighting simple

> lighting simple

> lighting soft

> surface dust #1 size 10.7

> volume #1 level 0.09513

> volume #1 level 0.115

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12
> 2020/Maps/DeepEMhancer/From
> Yogesh/deppEMhancer_J55-Cryosparc/J55_009_widetarget_maps.mrc"

Opened J55_009_widetarget_maps.mrc as #2, grid size 250,250,250, pixel 1.07,
shown at level 0.0457, step 1, values float32  

> volume #2 color #fafafa

> volume #2 color #b3b3b3

> surface dust #2 size 10.7

> volume #2 level 0.1126

> volume #2 level 0.02154

> volume #2 level 0.08851

> volume #1 level 0.1093

> save /Users/yogesh/Desktop/image1.png supersample 3

> close #2

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12
> 2020/Maps/Phenix/Job55/without model/No overall before/J55_iteration9_no
> overall_sharpened_map.ccp4"

Opened J55_iteration9_no overall_sharpened_map.ccp4 as #2, grid size
250,250,250, pixel 1.07, shown at level 3.95, step 1, values float32  

> volume #2 color #ededed

> volume #2 color #b3b3b3

> lighting soft

> lighting simple

> lighting soft

> surface dust #2 size 10.7

> volume #2 level 7.748

> volume #2 level 6.118

> volume #2 level 6.009

> save /Users/yogesh/Desktop/image1.png supersample 3

> save /Users/yogesh/Desktop/image1.png supersample 3

> save /Users/yogesh/Desktop/image1.png supersample 3

> close session

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12
> 2020/Maps/Phenix/Job36/without
> model/standard/Class-1/J36_class1_sharpened_map.ccp4"

Opened J36_class1_sharpened_map.ccp4 as #1, grid size 250,250,250, pixel 1.07,
shown at level 1.99, step 1, values float32  

> surface dust #1 size 10.7

> volume #1 level 3.037

> volume #1 level 5.539

> volume #1 level 2.828

> volume #1 level 4.288

> save /Users/yogesh/Desktop/image1.png supersample 3

> close session

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12
> 2020/Maps/Phenix/Job55/without model/No overall before/J55_iteration9_no
> overall_sharpened_map.ccp4"

Opened J55_iteration9_no overall_sharpened_map.ccp4 as #1, grid size
250,250,250, pixel 1.07, shown at level 3.95, step 1, values float32  

> lighting soft

> surface dust #1 size 10.7

> volume #1 level 4.434

> volume #1 level 6.009

> open "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/ISOLDE files/Final/J55_phenix-autosharpen-map_coot-
> itr5_rsr018_final_ISOLDE.pdb"

Chain information for J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb #2  
---  
Chain | Description  
A D | No description available  
B E | No description available  
C | No description available  
F G H I | No description available  
J | No description available  
  

> hide atoms

> show cartoons

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb  
---  
Chain | Description  
2.2/A 2.2/D | No description available  
2.2/B 2.2/E | No description available  
2.2/C | No description available  
2.2/F 2.2/G 2.2/H 2.2/I | No description available  
2.2/J | No description available  
  
Done loading forcefield  
ISOLDE: stopped sim  

> addh

Summary of feedback from adding hydrogens to J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb #2.2  
---  
notes | No usable SEQRES records for J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb (#2.2) chain A; guessing termini instead  
No usable SEQRES records for J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb (#2.2) chain B; guessing termini instead  
No usable SEQRES records for J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb (#2.2) chain C; guessing termini instead  
No usable SEQRES records for J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb (#2.2) chain D; guessing termini instead  
No usable SEQRES records for J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb (#2.2) chain E; guessing termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A PRO 31, /B PHE 39, /C ILE
35, /D PRO 31, /E PHE 39, /F MET 1, /G MET 1, /H MET 1, /I MET 1, /J MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASN 237, /B ASN 237, /C
ASN 237, /D ASN 237, /E ASN 237, /F GLY 89, /G GLY 89, /H GLY 89, /I GLY 89,
/J GLU 258  
1355 hydrogen bonds  
/A ASN 237 is not terminus, removing H atom from 'C'  
/B ASN 237 is not terminus, removing H atom from 'C'  
/C ASN 237 is not terminus, removing H atom from 'C'  
/D ASN 237 is not terminus, removing H atom from 'C'  
/E ASN 237 is not terminus, removing H atom from 'C'  
5 messages similar to the above omitted  
13723 hydrogens added  
  

Populating font family aliases took 820 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: started sim  

> volume hide

ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: stopped sim  

> save "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/ISOLDE files/Final/Fixing clashes_final_J55-phenix-
> autosharpenmap_coot-itr6_rsr-18.cxs"

Taking snapshot of stepper: J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb  

——— End of log from Thu Jul 29 16:49:45 2021 ———

opened ChimeraX session  

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  
Opened J55_iteration9_no overall_sharpened_map.ccp4 as #2.1.1.1, grid size
250,250,250, pixel 1.07, shown at step 1, values float32  

Populating font family aliases took 705 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: started sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: resumed sim  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: stopped sim  

> save "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/ISOLDE files/Final/ISOLDE_Fixed-clashes_final_J55-phenix-
> autosharpenmap_coot-itr6_rsr-18.pdb" relModel #2.2

ISOLDE: started sim  
ISOLDE: stopped sim  

> save "/Users/yogesh/Postdoc_GW/Collaborations/BacterialCORE/Data/Electron
> Microscopy/Cryo/8579/Processing_Data/BBK-Krios_14 12 2020/Model
> building/ISOLDE files/Final/Fixing clashes_final_J55-phenix-
> autosharpenmap_coot-itr6_rsr-18.cxs"

Taking snapshot of stepper: J55_phenix-autosharpen-map_coot-
itr5_rsr018_final_ISOLDE.pdb  

> close session

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/yogesh/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/validation/ramaplot.py", line 112, in
_selection_changed_cb  
residues = self.current_model.residues  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_  
return base.__getattr__(self, attr_name, look_in_class=base)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
AttributeError: Execution of 'Structure' object's 'residues' property raised
AttributeError  
  
Error processing trigger "selection changed":  
AttributeError: Execution of 'Structure' object's 'residues' property raised
AttributeError  
  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/attributes.py", line 83, in get_attr  
raise AttributeError("Execution of '%s' object's '%s' property raised
AttributeError" % (self.class_.__name__, attr_name)) from None  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.5.14
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 1554.120.19.0.0 (iBridge: 18.16.14663.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 11.4 (20F71)
      Kernel Version: Darwin 20.5.0
      Time since boot: 6 days 22:29

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
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    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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
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    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
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    netCDF4: 1.5.4
    networkx: 2.5
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    openvr: 1.14.1501
    packaging: 20.9
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