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Opened 5 years ago
Closed 5 years ago
#3719 closed defect (duplicate)
Nucleotides: asking for distance from None
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | 0.93 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
Can't save .cxs session file.
Log:
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open2 /Users/SYC/Desktop/Lig/Synaptic_Complex.cxs
Log from Tue Sep 15 13:22:54 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
> open2 /Users/SYC/Desktop/Lig/Synaptic_Complex.cxs
Log from Tue Sep 15 11:43:15 2020UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open2 /Users/SYC/Desktop/Lig/Lig.py
ChimeraX cannot open a regular Chimera session.
An exporter from Chimera to ChimeraX is being worked on but is not ready at
this time.
> open2 /Users/SYC/Desktop/postprocess_sortKu2_6p9A.mrc
> /Users/SYC/Desktop/postprocess_sortLigKu1_7p08A.mrc
> /Users/SYC/Desktop/postprocess_sortXXL_7p08A.mrc
Opened postprocess_sortKu2_6p9A.mrc, grid size 192,192,192, pixel 1.66, shown
at level 0.0145, step 1, values float32
Opened postprocess_sortLigKu1_7p08A.mrc, grid size 192,192,192, pixel 1.66,
shown at level 0.019, step 1, values float32
Opened postprocess_sortXXL_7p08A.mrc, grid size 192,192,192, pixel 1.66, shown
at level 0.0206, step 1, values float32
Expected an objects specifier or a view name or a keyword
> set bgColor white
> volume #1 color #b2b2b280
> color #1-3 #b2b2b280
> volume #1 level 0.02
> volume #2 level 0.02
> volume #3 level 0.02
> volume #1 level 0.03
> volume #2 level 0.03
> volume #3 level 0.03
> surface dust #1-3 size 5
> surface dust #1-3 size 10
> open2 "/Users/SYC/Box Sync/He Lab/Siyu Chen/DNA-
> PKcs_Cryo_Chimera/20feb14a_ADP_Combine/Deposit/XXL/postprocess_XXL.mrc"
Opened postprocess_XXL.mrc, grid size 216,216,216, pixel 2.2, shown at level
0.00335, step 1, values float32
> volume #4 level 0.003
> volume #4 level 0.03
> toolshed show Toolbar
> lighting full
> graphics silhouettes true
Empty filename passed to function
> save2 /Users/SYC/Desktop/Lig/Synaptic_Complex.cxs
> open2 "/Users/SYC/Box Sync/He Lab/Siyu Chen/DNA-
> PKcs_Cryo_Chimera/20feb14a_ADP_Combine/Deposit/Compose/FULL.pdb"
Chain information for FULL.pdb #4
---
Chain | Description
A J | No description available
B K | No description available
C L | No description available
D M | No description available
E N | No description available
F P | No description available
G O | No description available
H | No description available
I | No description available
X Y | No description available
> hide #4
> show #4 cartoons
> select #4
92764 atoms, 94889 bonds, 88 pseudobonds, 2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> select clear
> toolshed show "Fit in Map"
Fit molecule FULL.pdb (#4) to map postprocess_sortXXL_7p08A.mrc (#3) using
92764 atoms
average map value = 0.005361, steps = 632
shifted from previous position = 97.3
rotated from previous position = 45.7 degrees
atoms outside contour = 86207, contour level = 0.03
Position of FULL.pdb (#4) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
-0.53697665 0.84359343 0.00248314 85.42184855
-0.84356455 -0.53692777 -0.01036137 490.62559636
-0.00740751 -0.00765850 0.99994322 -100.53882950
Axis 0.00160200 0.00586221 -0.99998153
Axis point 177.10984972 221.62067207 0.00000000
Rotation angle (degrees) 122.47833171
Shift along axis 103.54996658
Expected an objects specifier or a view name or a keyword
> view name DEF
> select clear
> color #4 gray
Unknown command: copy #4
> open2 "/Users/SYC/Box Sync/He Lab/Siyu Chen/DNA-
> PKcs_Cryo_Chimera/20feb14a_ADP_Combine/Deposit/Compose/FULL.pdb"
Chain information for FULL.pdb #5
---
Chain | Description
A J | No description available
B K | No description available
C L | No description available
D M | No description available
E N | No description available
F P | No description available
G O | No description available
H | No description available
I | No description available
X Y | No description available
> close #5
> select #5/H:1-300
Nothing selected
> save KXXL.pdb #4/A,B,D,E,J,K,M,N,X,Y,F,G,P,O,H,I relModel #3
> open2 /Users/SYC/Desktop/KXXL.pdb
Chain information for KXXL.pdb #5
---
Chain | Description
A J | No description available
B K | No description available
C L | No description available
D M | No description available
E N | No description available
F P | No description available
G O | No description available
H | No description available
I | No description available
X Y | No description available
> select #4/A,B,D,E,J,K,M,N,X,Y,F,G,P,O,H,I
33268 atoms, 34171 bonds, 28 pseudobonds, 2 models selected
> close #5
> save KXXL.pdb #4 selectedOnly true relModel #3
> select clear
> open2 /Users/SYC/Desktop/KXXL.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/SYC/Desktop/KXXL.pdb" mode="rt" encoding="utf-8">
---
warnings | Start residue of secondary structure not found: HELIX 39 39 GLN C
16 LEU C 19 1 4
Start residue of secondary structure not found: HELIX 40 40 SER C 20 ALA C 22
1 3
Start residue of secondary structure not found: HELIX 41 41 LEU C 29 VAL C 43
1 15
Start residue of secondary structure not found: HELIX 42 42 VAL C 50 VAL C 58
1 9
Start residue of secondary structure not found: HELIX 43 43 LEU C 65 PHE C 68
1 4
617 messages similar to the above omitted
Chain information for KXXL.pdb #5
---
Chain | Description
A J | No description available
B K | No description available
D M | No description available
E N | No description available
F P | No description available
G O | No description available
H | No description available
I | No description available
X Y | No description available
> hide #!4 models
> color #5/A,B,J,K red
> hide #5
> show #5 cartoons
> color #5/D,E,M,N cyan
> show #5/D,E,M,N
> nucleotides ladder
> color #5/H,I blue
> color #5/X,Y green
> toolshed show "Fit in Map"
> color #5/F,G,O,P yellow
Drag select of 9 residues
> delete sel
Drag select of 9 residues
> delete sel
> view DEF
> view DEF
> save2 /Users/SYC/Desktop/Lig/Synaptic_Complex.cxs
opened ChimeraX session
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 525, in rebuild
_rebuild_molecule('internal', mol)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "new frame":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
> toolshed show "Fit in Map"
> select #5/J,K,M,N
9468 atoms, 9779 bonds, 4 pseudobonds, 2 models selected
> select #5/J,K,M,N,H:294-300
169 atoms, 170 bonds, 1 model selected
> select #5/J,K,M,N/H:294-300
9525 atoms, 9837 bonds, 4 pseudobonds, 2 models selected
Fit molecule KXXL.pdb (#5) to map postprocess_sortKu2_6p9A.mrc (#1) using 9525
atoms
average map value = 0.03792, steps = 140
shifted from previous position = 26.9
rotated from previous position = 20.1 degrees
atoms outside contour = 3332, contour level = 0.03
> hide #5/M,N
> show #5/M,N
> select clear
> select #5/A,B,E,D/I:294-300
9525 atoms, 9837 bonds, 4 pseudobonds, 2 models selected
> toolshed show "Fit in Map"
Fit molecule KXXL.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
9525 atoms
average map value = 0.0372, steps = 164
shifted from previous position = 29.5
rotated from previous position = 22.9 degrees
atoms outside contour = 3585, contour level = 0.03
> hide #5/D,E
> show #5/D,E
> select clear
Expected an objects specifier or a keyword
> select #5/I:294-300
57 atoms, 58 bonds, 1 model selected
Fit molecule KXXL.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
57 atoms
average map value = 0.03114, steps = 68
shifted from previous position = 2.97
rotated from previous position = 30.4 degrees
atoms outside contour = 23, contour level = 0.03
Fit molecule KXXL.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
57 atoms
average map value = 0.03114, steps = 68
shifted from previous position = 2.97
rotated from previous position = 30.4 degrees
atoms outside contour = 23, contour level = 0.03
> select clear
> select #5/H:294-300
57 atoms, 58 bonds, 1 model selected
> view sel
> toolshed show "Fit in Map"
Fit molecule KXXL.pdb (#5) to map postprocess_sortKu2_6p9A.mrc (#1) using 57
atoms
average map value = 0.0322, steps = 100
shifted from previous position = 1.06
rotated from previous position = 43 degrees
atoms outside contour = 21, contour level = 0.03
> select clear
> view DEF
> view DEF
> save2 /Users/SYC/Desktop/Lig/Synaptic_Complex.cxs
> select #5/B,K:544-554
184 atoms, 184 bonds, 1 model selected
> cartoon hide sel
> save2 /Users/SYC/Desktop/Lig/Synaptic_Complex.cxs
> open 3ii6
Summary of feedback from opening 3ii6 fetched from pdb
---
notes | Fetching compressed mmCIF 3ii6 from
http://files.rcsb.org/download/3ii6.cif
| Summary of feedback from opening /Users/SYC/Downloads/ChimeraX/PDB/3ii6.cif
---
note | Fetching CCD CL from http://ligand-expo.rcsb.org/reports/C/CL/CL.cif
3ii6 title:
Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA
LigaseIV. [more info...]
Chain information for 3ii6 #6
---
Chain | Description
A B C D | DNA repair protein XRCC4
X Y | DNA ligase 4
Non-standard residues in 3ii6 #6
---
CL — chloride ion
3ii6 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> close #6
> open 3ii6.pdb1
File not found: 3ii6.pdb1
> open 3ii6 maxModels 1
3ii6 title:
Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA
LigaseIV. [more info...]
Chain information for 3ii6 #6
---
Chain | Description
A B C D | DNA repair protein XRCC4
X Y | DNA ligase 4
Non-standard residues in 3ii6 #6
---
CL — chloride ion
3ii6 mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> hide #6
> show #6 cartoons
> delete #6/C,D,Y
> matchmaker #6 to #5/F,G,X
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 KXXL.pdb, chain X (#5) with 3ii6, chain X (#6), sequence alignment
score = 1228.5
RMSD between 127 pruned atom pairs is 0.569 angstroms; (across all 254 pairs:
9.595)
> hide #!5 models
> toolshed show "Fit in Map"
Fit molecule 3ii6 (#6) to map postprocess_sortXXL_7p08A.mrc (#3) using 5470
atoms
average map value = 0.02552, steps = 128
shifted from previous position = 0.691
rotated from previous position = 10.7 degrees
atoms outside contour = 3568, contour level = 0.03
Position of 3ii6 (#6) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
0.16769537 -0.89086334 -0.42218570 247.28810140
0.58972250 -0.25252896 0.76710918 94.12820306
-0.79000356 -0.37761307 0.48301422 205.38809337
Axis -0.60017778 0.19284687 0.77627104
Axis point 161.25415108 146.58152959 -0.00000000
Rotation angle (degrees) 107.51224917
Shift along axis 29.17233462
> close #6
> view DEF
> open 1ik9
Summary of feedback from opening 1ik9 fetched from pdb
---
note | Fetching compressed mmCIF 1ik9 from
http://files.rcsb.org/download/1ik9.cif
1ik9 title:
Crystal structure of A XRCC4-DNA ligase IV complex [more info...]
Chain information for 1ik9 #6
---
Chain | Description
A B | DNA repair protein XRCC4
C | DNA ligase IV
> select up
314 atoms, 318 bonds, 1 model selected
> matchmaker #6 to #5/F,G
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 KXXL.pdb, chain F (#5) with 1ik9, chain B (#6), sequence alignment
score = 1015.1
RMSD between 131 pruned atom pairs is 0.938 angstroms; (across all 195 pairs:
2.823)
> toolshed show "Fit in Map"
Fit molecule 1ik9 (#6) to map postprocess_sortXXL_7p08A.mrc (#3) using 3736
atoms
average map value = 0.03493, steps = 56
shifted from previous position = 1.47
rotated from previous position = 4.02 degrees
atoms outside contour = 1908, contour level = 0.03
Position of 1ik9 (#6) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
0.84829878 -0.52313969 0.08193930 219.83967763
0.42900685 0.76970627 0.47276355 52.24387523
-0.31039057 -0.36589223 0.87737140 149.18112242
Axis -0.63147042 0.29540690 0.71692389
Axis point 70.81182455 379.85574824 0.00000000
Rotation angle (degrees) 41.60948018
Shift along axis -16.43754096
> toolshed show "Fit in Map"
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 228, in toggle_panel_display
_resize_dock_widget(self)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 238, in _resize_dock_widget
p.window().resizeDocks([p], [p.widget().sizeHint().height()], Qt.Vertical)
AttributeError: 'QDockWidget' object has no attribute 'resizeDocks'
AttributeError: 'QDockWidget' object has no attribute 'resizeDocks'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 238, in _resize_dock_widget
p.window().resizeDocks([p], [p.widget().sizeHint().height()], Qt.Vertical)
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 228, in toggle_panel_display
_resize_dock_widget(self)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 238, in _resize_dock_widget
p.window().resizeDocks([p], [p.widget().sizeHint().height()], Qt.Vertical)
AttributeError: 'QDockWidget' object has no attribute 'resizeDocks'
AttributeError: 'QDockWidget' object has no attribute 'resizeDocks'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/composite.py", line 238, in _resize_dock_widget
p.window().resizeDocks([p], [p.widget().sizeHint().height()], Qt.Vertical)
See log for complete Python traceback.
Fit molecule 1ik9 (#6) to map postprocess_sortXXL_7p08A.mrc (#3) using 3736
atoms
average map value = 0.03493, steps = 28
shifted from previous position = 0.0562
rotated from previous position = 0.0606 degrees
atoms outside contour = 1909, contour level = 0.03
Position of 1ik9 (#6) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
0.84833241 -0.52302746 0.08230674 219.79615601
0.42907939 0.77020938 0.47187751 52.35322629
-0.31019832 -0.36499286 0.87781388 149.10581204
Axis -0.63065003 0.29578455 0.71749010
Axis point 70.53158586 380.31569024 0.00000000
Rotation angle (degrees) 41.56721780
Shift along axis -16.14723157
> select #6
3736 atoms, 3570 bonds, 2 pseudobonds, 2 models selected
> select clear
> select #6
3736 atoms, 3570 bonds, 2 pseudobonds, 2 models selected
> toolshed show Toolbar
> ui mousemode rightMode "rotate selected models"
Fit molecule 1ik9 (#6) to map postprocess_sortXXL_7p08A.mrc (#3) using 3736
atoms
average map value = 0.01885, steps = 104
shifted from previous position = 3.59
rotated from previous position = 5.36 degrees
atoms outside contour = 2738, contour level = 0.03
Position of 1ik9 (#6) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
-0.63630729 0.26480857 0.72456157 155.36216054
0.05139216 -0.92260016 0.38231897 83.83574203
0.76972195 0.28050913 0.57344812 168.17210798
Axis -0.42292007 -0.18759713 -0.88653592
Axis point 38.95076975 22.15328818 0.00000000
Rotation angle (degrees) 173.08681162
Shift along axis -230.52373400
> ui mousemode rightMode "translate selected models"
Fit molecule 1ik9 (#6) to map postprocess_sortXXL_7p08A.mrc (#3) using 3736
atoms
average map value = 0.03076, steps = 112
shifted from previous position = 6.77
rotated from previous position = 15.6 degrees
atoms outside contour = 2104, contour level = 0.03
Position of 1ik9 (#6) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
-0.69213137 0.45766933 0.55811554 150.19648243
-0.16760597 -0.85403370 0.49247810 79.46642787
0.70204160 0.24731605 0.66781163 159.77026906
Axis -0.35692720 -0.20953947 -0.91032751
Axis point 47.10974699 14.22416752 0.00000000
Rotation angle (degrees) 159.91375411
Shift along axis -215.70383546
Fit molecule 1ik9 (#6) to map postprocess_sortXXL_7p08A.mrc (#3) using 3736
atoms
average map value = 0.03493, steps = 28
shifted from previous position = 0.0497
rotated from previous position = 0.0308 degrees
atoms outside contour = 1912, contour level = 0.03
Position of 1ik9 (#6) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
0.84829222 -0.52312438 0.08210482 219.83279739
0.42908724 0.76993374 0.47231999 52.28108915
-0.31029737 -0.36543524 0.87759480 149.14743783
Axis -0.63103012 0.29557273 0.71724316
Axis point 70.71733465 380.06808759 0.00000000
Rotation angle (degrees) 41.59030880
Shift along axis -16.29327187
> select clear
> show #!5 models
> close #6
> view DEF
> select clear
> save2 /Users/SYC/Desktop/Lig/Synaptic_Complex.cxs
opened ChimeraX session
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke
return self._func(self._name, data)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 525, in rebuild
_rebuild_molecule('internal', mol)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 652, in _rebuild_molecule
hide_residues = make_ladder(nd, residues, mol._ladder_params)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 1237, in make_ladder
va, na, ta = get_cylinder(params.rung_radius, ep0, ep1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/nucleotides/_data.py", line 733, in get_cylinder
h = distance(p0, p1)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 71, in distance
return sqrt(distance_squared(p, q))
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
TypeError: object of type 'NoneType' has no len()
Error processing trigger "new frame":
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/geometry/vector.py", line 63, in distance_squared
if len(p) == 3:
See log for complete Python traceback.
> close #5
> open2 /Users/SYC/Desktop/right.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/SYC/Desktop/right.pdb" mode="rt" encoding="utf-8">
---
warnings | Start residue of secondary structure not found: HELIX 46 46 GLU H 2
GLY H 7 1 6
Start residue of secondary structure not found: HELIX 47 47 LEU H 8 MSE H 10 1
3
Start residue of secondary structure not found: HELIX 48 48 THR H 51 LEU H 61
1 11
Start residue of secondary structure not found: HELIX 49 49 PRO H 69 LEU H 83
1 15
Start residue of secondary structure not found: HELIX 50 50 PRO H 128 LEU H
135 1 8
141 messages similar to the above omitted
Chain information for right.pdb #5
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
X | No description available
> hide #5
> show #5 cartoons
> select #5
28990 atoms, 29402 bonds, 8 pseudobonds, 2 models selected
> toolshed show Toolbar
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> toolshed show "Fit in Map"
Fit molecule right.pdb (#5) to map postprocess_sortKu2_6p9A.mrc (#1) using
28990 atoms
average map value = 0.02596, steps = 348
shifted from previous position = 15
rotated from previous position = 53.2 degrees
atoms outside contour = 16392, contour level = 0.03
Position of right.pdb (#5) relative to postprocess_sortKu2_6p9A.mrc (#1)
coordinates:
Matrix rotation and translation
-0.98084522 -0.08546289 -0.17503923 350.70763307
0.09266843 -0.99513671 -0.03339895 304.73820640
-0.17133359 -0.04897981 0.98399481 40.50579412
Axis -0.08711698 -0.02071927 0.99598260
Axis point 170.26967703 160.68515994 0.00000000
Rotation angle (degrees) 174.86947611
Shift along axis 3.47652232
Expected an objects specifier or a keyword
> select #5/X,F,G
10517 atoms, 10621 bonds, 4 pseudobonds, 2 models selected
Fit molecule right.pdb (#5) to map postprocess_sortKu2_6p9A.mrc (#1) using
10517 atoms
average map value = 0.01105, steps = 2000
shifted from previous position = 4.03
rotated from previous position = 4.34 degrees
atoms outside contour = 8741, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortKu2_6p9A.mrc (#1) using
10517 atoms
average map value = 0.01105, steps = 2000
shifted from previous position = 4.03
rotated from previous position = 4.34 degrees
atoms outside contour = 8741, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortXXL_7p08A.mrc (#3) using
10517 atoms
average map value = 0.03206, steps = 100
shifted from previous position = 7.86
rotated from previous position = 11.5 degrees
atoms outside contour = 5624, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortXXL_7p08A.mrc (#3) using
10517 atoms
average map value = 0.03206, steps = 100
shifted from previous position = 7.86
rotated from previous position = 11.5 degrees
atoms outside contour = 5624, contour level = 0.03
Position of right.pdb (#5) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
-0.99984030 0.01424735 -0.01078753 319.39681028
-0.01434325 -0.99985783 0.00886523 320.45773299
-0.01065969 0.00901855 0.99990251 2.32407916
Axis 0.00536235 -0.00447130 -0.99997563
Axis point 160.84997794 159.08204924 0.00000000
Rotation angle (degrees) 179.18089189
Shift along axis -2.04416721
Fit molecule right.pdb (#5) to map postprocess_sortXXL_7p08A.mrc (#3) using
10517 atoms
average map value = 0.03206, steps = 100
shifted from previous position = 7.86
rotated from previous position = 11.5 degrees
atoms outside contour = 5624, contour level = 0.03
Position of right.pdb (#5) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
-0.99984030 0.01424735 -0.01078753 319.39681028
-0.01434325 -0.99985783 0.00886523 320.45773299
-0.01065969 0.00901855 0.99990251 2.32407916
Axis 0.00536235 -0.00447130 -0.99997563
Axis point 160.84997794 159.08204924 0.00000000
Rotation angle (degrees) 179.18089189
Shift along axis -2.04416721
Fit molecule right.pdb (#5) to map postprocess_sortXXL_7p08A.mrc (#3) using
10517 atoms
average map value = 0.03206, steps = 40
shifted from previous position = 0.0049
rotated from previous position = 0.00567 degrees
atoms outside contour = 5624, contour level = 0.03
> select #5/A,B,E,D
18473 atoms, 18781 bonds, 4 pseudobonds, 2 models selected
Fit molecule right.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
18473 atoms
average map value = 0.01678, steps = 272
shifted from previous position = 70.3
rotated from previous position = 22.3 degrees
atoms outside contour = 14997, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
18473 atoms
average map value = -0.0001379, steps = 244
shifted from previous position = 9.96
rotated from previous position = 15 degrees
atoms outside contour = 18473, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
18473 atoms
average map value = -0.0001919, steps = 216
shifted from previous position = 5.92
rotated from previous position = 4.39 degrees
atoms outside contour = 18473, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
18473 atoms
average map value = 0.0003972, steps = 176
shifted from previous position = 31.3
rotated from previous position = 13.2 degrees
atoms outside contour = 18470, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
18473 atoms
average map value = -0.0002802, steps = 252
shifted from previous position = 4.11
rotated from previous position = 13.5 degrees
atoms outside contour = 18473, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
18473 atoms
average map value = -0.0003674, steps = 2000
shifted from previous position = 4.3
rotated from previous position = 8.84 degrees
atoms outside contour = 18473, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
18473 atoms
average map value = -0.0003074, steps = 632
shifted from previous position = 2
rotated from previous position = 6.98 degrees
atoms outside contour = 18473, contour level = 0.03
Fit molecule right.pdb (#5) to map postprocess_sortLigKu1_7p08A.mrc (#2) using
18473 atoms
average map value = -0.0003413, steps = 92
shifted from previous position = 3.95
rotated from previous position = 1.3 degrees
atoms outside contour = 18473, contour level = 0.03
> ui mousemode rightMode "translate selected models"
> close #5
> open2 /Users/SYC/Desktop/KXXL.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/SYC/Desktop/KXXL.pdb" mode="rt" encoding="utf-8">
---
warnings | Start residue of secondary structure not found: HELIX 39 39 GLN C
16 LEU C 19 1 4
Start residue of secondary structure not found: HELIX 40 40 SER C 20 ALA C 22
1 3
Start residue of secondary structure not found: HELIX 41 41 LEU C 29 VAL C 43
1 15
Start residue of secondary structure not found: HELIX 42 42 VAL C 50 VAL C 58
1 9
Start residue of secondary structure not found: HELIX 43 43 LEU C 65 PHE C 68
1 4
617 messages similar to the above omitted
Chain information for KXXL.pdb #5
---
Chain | Description
A J | No description available
B K | No description available
D M | No description available
E N | No description available
F P | No description available
G O | No description available
H | No description available
I | No description available
X Y | No description available
> select #5
33268 atoms, 34171 bonds, 28 pseudobonds, 2 models selected
> close #5
> open2 /Users/SYC/Desktop/Lig/KXXL_Right_fit.cif
Summary of feedback from opening /Users/SYC/Desktop/Lig/KXXL_Right_fit.cif
---
warnings | Unknown polymer entity '1' near line 166
Unknown polymer entity '2' near line 8250
Unknown polymer entity '3' near line 16728
Unknown polymer entity '4' near line 17715
Unknown polymer entity '5' near line 18639
4 messages similar to the above omitted
Atom H1 is not in the residue template for TYR #32 in chain A
Atom H1 is not in the residue template for SER #4 in chain B
Atom H is not in the residue template for DT #1 in chain D
Atom H1 is not in the residue template for MET #1 in chain F
Atom H1 is not in the residue template for MET #1 in chain G
Atom H1 is not in the residue template for MSE #1 in chain H
Atom H1 is not in the residue template for MSE #1 in chain I
Atom H1 is not in the residue template for TYR #32 in chain J
1 messages similar to the above omitted
Atom H is not in the residue template for DT #1 in chain M
Atom H is not in the residue template for DG #1 in chain N
Atom H1 is not in the residue template for MET #1 in chain O
Atom H1 is not in the residue template for MET #1 in chain P
Atom H1 is not in the residue template for SER #656 in chain X
Atom H1 is not in the residue template for SER #656 in chain Y
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for KXXL_Right_fit.cif #5
---
Chain | Description
A J | ?
B K | ?
D M | ?
E | ?
F P | ?
G O | ?
H | ?
I | ?
N | ?
X Y | ?
> hide #5
> show #5 cartoons
> select #5/A,B,E,D
18473 atoms, 18781 bonds, 4 pseudobonds, 2 models selected
> select up
65178 atoms, 66080 bonds, 24 pseudobonds, 2 models selected
> select up
65178 atoms, 66080 bonds, 24 pseudobonds, 2 models selected
> select #5/A,B,E,D
18473 atoms, 18781 bonds, 4 pseudobonds, 2 models selected
> save Ku1.pdb #5 selectedOnly true
> open2 /Users/SYC/Desktop/Ku1.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/SYC/Desktop/Ku1.pdb" mode="rt" encoding="utf-8">
---
warnings | Start residue of secondary structure not found: HELIX 39 39 LEU F
28 SER F 30 1 3
Start residue of secondary structure not found: HELIX 40 40 GLU F 49 MET F 59
1 11
Start residue of secondary structure not found: HELIX 41 41 LYS F 65 LEU F 74
1 10
Start residue of secondary structure not found: HELIX 42 42 PRO F 119 ASN F
200 1 82
Start residue of secondary structure not found: HELIX 43 43 GLU G 49 ASP G 58
1 10
183 messages similar to the above omitted
Chain information for Ku1.pdb #6
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
> select #5
65178 atoms, 66080 bonds, 24 pseudobonds, 2 models selected
> ~select #5
Nothing selected
> select #6
18473 atoms, 18781 bonds, 4 pseudobonds, 2 models selected
> hide #!5 models
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> toolshed show "Fit in Map"
Fit molecule Ku1.pdb (#6) to map postprocess_sortKu2_6p9A.mrc (#1) using 18473
atoms
average map value = 0.03448, steps = 332
shifted from previous position = 29
rotated from previous position = 87.3 degrees
atoms outside contour = 7679, contour level = 0.03
Position of Ku1.pdb (#6) relative to postprocess_sortKu2_6p9A.mrc (#1)
coordinates:
Matrix rotation and translation
-0.98054033 -0.08604929 -0.17645428 350.86171895
0.09345088 -0.99504114 -0.03405855 304.72624040
-0.17264857 -0.04988559 0.98371938 40.80576959
Axis -0.08781253 -0.02111506 0.99591321
Axis point 170.32063094 160.75584470 0.00000000
Rotation angle (degrees) 174.82958242
Shift along axis 3.39463758
> select clear
> color #5/A,B red
> color #6/A,B red
> color #6/D,E cyan
> select clear
> hide #!6 models
> show #!5 models
> select #5/F,G,X
10517 atoms, 10621 bonds, 4 pseudobonds, 2 models selected
> save X4L41.pdb #5 selectedOnly true
> open2 /Users/SYC/Desktop/X4L41.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/SYC/Desktop/X4L41.pdb" mode="rt" encoding="utf-8">
---
warnings | Start residue of secondary structure not found: HELIX 1 1 LYS A 46
PHE A 49 1 4
Start residue of secondary structure not found: HELIX 2 2 PHE A 60 SER A 77 1
18
Start residue of secondary structure not found: HELIX 3 3 ALA A 113 LEU A 119
1 7
Start residue of secondary structure not found: HELIX 4 4 ASP A 120 PHE A 122
1 3
Start residue of secondary structure not found: HELIX 5 5 GLN A 125 MET A 135
1 11
211 messages similar to the above omitted
Chain information for X4L41.pdb #7
---
Chain | Description
F | No description available
G | No description available
X | No description available
> hide #!5 models
> select clear
> select #7
10517 atoms, 10621 bonds, 4 pseudobonds, 2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> toolshed show "Fit in Map"
Fit molecule X4L41.pdb (#7) to map postprocess_sortXXL_7p08A.mrc (#3) using
10517 atoms
average map value = 0.03149, steps = 132
shifted from previous position = 26.5
rotated from previous position = 8.73 degrees
atoms outside contour = 5741, contour level = 0.03
Position of X4L41.pdb (#7) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
-0.99997844 0.00370940 -0.00541874 319.55044576
-0.00376194 -0.99994570 0.00971878 317.92682140
-0.00538239 0.00973895 0.99993809 1.21360696
Axis 0.00270034 -0.00486452 -0.99998452
Axis point 160.07378049 158.66201005 0.00000000
Rotation angle (degrees) 179.78595808
Shift along axis -1.89725606
> ~select #7
Nothing selected
> select clear
> show #!6 models
> show #!5 models
> hide #!5 models
Missing or invalid "models" argument: empty atom specifier
> hide #!7 models
> hide #!6 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!7 models
> hide #!7 models
> show #!6 models
> select #5@H
3629 atoms, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select clear
> select clear
> select clear
> select clear
> select #5/M:27
32 atoms, 34 bonds, 1 model selected
> select clear
> delete #5/J,K,M,N,P,O,Y
> show #!7 models
> save rest.pdb models #5
> close #6-7
> close #5
> open2 /Users/SYC/Desktop/Ku1.pdb /Users/SYC/Desktop/rest.pdb
> /Users/SYC/Desktop/X4L41.pdb
Chain information for Ku1.pdb #5
---
Chain | Description
J | No description available
K | No description available
M | No description available
N | No description available
Chain information for rest.pdb #6
---
Chain | Description
A | No description available
B | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
X | No description available
Chain information for X4L41.pdb #7
---
Chain | Description
O | No description available
P | No description available
Y | No description available
> select #6,7
44645 atoms, 45236 bonds, 20 pseudobonds, 4 models selected
> select #5,7
28990 atoms, 29402 bonds, 8 pseudobonds, 4 models selected
Expected an axis vector or a keyword
Expected an axis vector or a keyword
> roll models sel angle 180 frames 1
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> toolshed show "Fit in Map"
Fit molecule Ku1.pdb (#5) to map postprocess_sortKu2_6p9A.mrc (#1) using 18473
atoms
average map value = 0.03448, steps = 84
shifted from previous position = 8.83
rotated from previous position = 9.78 degrees
atoms outside contour = 7676, contour level = 0.03
Position of Ku1.pdb (#5) relative to postprocess_sortKu2_6p9A.mrc (#1)
coordinates:
Matrix rotation and translation
-0.98051604 -0.08626849 -0.17648242 350.89329867
0.09365929 -0.99502460 -0.03397036 304.69081686
-0.17267377 -0.04983770 0.98371743 40.81207540
Axis -0.08782682 -0.02108111 0.99591266
Axis point 170.32126156 160.75729110 0.00000000
Rotation angle (degrees) 174.81722901
Shift along axis 3.40419918
Fit molecule X4L41.pdb (#7) to map postprocess_sortXXL_7p08A.mrc (#3) using
10517 atoms
average map value = 0.03149, steps = 68
shifted from previous position = 7.32
rotated from previous position = 2.96 degrees
atoms outside contour = 5736, contour level = 0.03
Position of X4L41.pdb (#7) relative to postprocess_sortXXL_7p08A.mrc (#3)
coordinates:
Matrix rotation and translation
-0.99997874 0.00373318 -0.00534716 319.54584132
-0.00378288 -0.99994946 0.00931522 318.03659738
-0.00531212 0.00933525 0.99994233 1.26351089
Axis 0.00266490 -0.00466264 -0.99998558
Axis point 160.07340355 158.71512266 0.00000000
Rotation angle (degrees) 179.78467701
Shift along axis -1.89482685
> select clear
> save Lig_no_Cata.pdb #5-7
> open2 /Users/SYC/Desktop/Lig_no_Cata.pdb
Chain information for Lig_no_Cata.pdb
---
Chain | Description
8.2/A 8.1/J | No description available
8.2/B 8.1/K | No description available
8.2/D 8.1/M | No description available
8.2/E 8.1/N | No description available
8.2/F 8.3/P | No description available
8.2/G 8.3/O | No description available
8.2/H | No description available
8.2/I | No description available
8.2/X 8.3/Y | No description available
> hide #!6 models
> hide #!7 models
> hide #!5 models
> hide #!8 models
> show #!8 models
> close #5-7
> close #8
> open2 /Users/SYC/Desktop/Lig_no_Cata_1.pdb
Chain information for Lig_no_Cata_1.pdb #5
---
Chain | Description
A J | No description available
B K | No description available
D M | No description available
E N | No description available
F P | No description available
G O | No description available
H | No description available
I | No description available
X Y | No description available
> hide #5
> show #5 cartoons
> show #5/D,E,M,N
> color #5/A,B,J,K red
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> color #5/X,Y green
> color #5/H,I blue
> color #5/D,E,M,N cyan
> color #5/F,G,O,P yellow
> view DEF
> view DEF
> select clear
> hide #!5 models
> show #!5 models
> nucleotides ladder
> hide #!5 models
> show #!5 models
> show #5/D,E,M,N
> hide #5/D,E,M,N
> show #5/D,E,M,N
> select clear
Expected ',' or a keyword
> hide #5/B,N:544-551 cartoons
> show #5/B,N:544-551 cartoons
> show #5/B,K:544-555 cartoons
> hide #5/B,K:544-555 cartoons
> select clear
> lighting full
> lighting shadows false
> hide #!5 models
Missing or invalid "surfaces" argument: invalid surfaces specifier
Missing or invalid "surfaces" argument: only initial part "#1-3" of atom
specifier valid
> surface dust #1-3 size 10
> save2 /Users/SYC/Desktop/Lig/Combine/Local.png width 1280 height 517
> supersample 3
> show #!5 models
> open 6ERG
Summary of feedback from opening 6ERG fetched from pdb
---
notes | Fetching compressed mmCIF 6erg from
http://files.rcsb.org/download/6erg.cif
| Summary of feedback from opening /Users/SYC/Downloads/ChimeraX/PDB/6erg.cif
---
note | Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif
6erg title:
Complex of XLF and heterodimer Ku bound to DNA [more info...]
Chain information for 6erg #6
---
Chain | Description
A D | X-ray repair cross-complementing protein 6
B E | X-ray repair cross-complementing protein 5
C F | Non-homologous end-joining factor 1
H K | DNA (21-mer)
M R | DNA (34-mer)
Non-standard residues in 6erg #6
---
SO4 — sulfate ion
6erg mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> view DEF
> close #6
> open 6ERH
Summary of feedback from opening 6ERH fetched from pdb
---
note | Fetching compressed mmCIF 6erh from
http://files.rcsb.org/download/6erh.cif
6erh title:
Complex of XLF and heterodimer Ku bound to DNA [more info...]
Chain information for 6erh #6
---
Chain | Description
A C | X-ray repair cross-complementing protein 6
B D | X-ray repair cross-complementing protein 5
F O | DNA (34-mer)
K R | DNA (21-mer)
M T | Non-homologous end-joining factor 1
Non-standard residues in 6erh #6
---
SO4 — sulfate ion
6erh mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> close #6
> open 6bkf
Summary of feedback from opening 6bkf fetched from pdb
---
notes | Fetching compressed mmCIF 6bkf from
http://files.rcsb.org/download/6bkf.cif
| Summary of feedback from opening /Users/SYC/Downloads/ChimeraX/PDB/6bkf.cif
---
note | Fetching CCD AMP from http://ligand-expo.rcsb.org/reports/A/AMP/AMP.cif
6bkf title:
Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate
in open conformation [more info...]
Chain information for 6bkf #6
---
Chain | Description
A | DNA ligase 4
D | DNA (5'-D(P*GP*TP*CP*GP*GP*ap*C)-3')
P | DNA (5'-D(*GP*CP*TP*GP*ap*TP*GP*CP*GP*TP*C)-3')
T | DNA (5'-D(*GP*TP*CP*CP*GP*ap*CP*GP*ap*CP*GP*CP*ap*TP*CP*ap*GP*C)-3')
Non-standard residues in 6bkf #6
---
AMP — adenosine monophosphate
> select #6
4861 atoms, 5035 bonds, 53 pseudobonds, 3 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> toolshed show "Fit in Map"
Fit molecule 6bkf (#6) to map postprocess_sortLigKu1_7p08A.mrc (#2) using 4861
atoms
average map value = 0.02894, steps = 172
shifted from previous position = 13.7
rotated from previous position = 35.8 degrees
atoms outside contour = 2600, contour level = 0.03
Position of 6bkf (#6) relative to postprocess_sortLigKu1_7p08A.mrc (#2)
coordinates:
Matrix rotation and translation
0.27385379 -0.58988841 -0.75962870 147.72770072
0.93391073 0.35182633 0.06347407 156.12692039
0.22981476 -0.72680802 0.64725211 95.08601194
Axis -0.39887260 -0.49939369 0.76909466
Axis point 5.82853571 200.14284278 0.00000000
Rotation angle (degrees) 82.15659286
Shift along axis -63.76318749
> select clear
> color #6 green
> color #6/B,C,D cyan
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #6/D,P,T cyan
> select clear
> nucleotides stubs
> hide #5/D,E,M,N
> show #5/D,E,M,N
> nucleotides ladder
> hide #5/D,E,M,N
> show #5/D,E,M,N
> nucleotides #!5-6 slab
> style nucleic & #!5-6 stick
Changed 4553 atom styles
> nucleotides #!5-6 stubs
> select all
160743 atoms, 163941 bonds, 165 pseudobonds, 13 models selected
> nucleotides sel slab
> style nucleic & sel stick
Changed 7053 atom styles
> nucleotides sel slab
> style nucleic & sel stick
Changed 7053 atom styles
> nucleotides sel stubs
> color sel bynucleotide
> select #5/D,E,M,N
3821 atoms, 4115 bonds, 1 model selected
> color sel cyan
> hide sel
> show sel
> nucleotides sel slab
> style nucleic & sel stick
Changed 3821 atom styles
> hide sel
> show sel
> hide #6/D,P,T cartoons
> hide #6/D,P,T
> select clear
> view DEF
> select clear
> save2 /Users/SYC/Desktop/Lig/Synaptic_Complex.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 564, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e30ef10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x16de49790> 'Ku1.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'Ku1.pdb'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1373, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog
_dlg.display(session, session.ui.main_window)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display
run(session, cmd)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save
mgr).save(session, path, **provider_kw)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 564, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e30ef10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x16de49790> 'Ku1.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'Ku1.pdb'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
> view DEF
> save2 /Users/SYC/Desktop/Lig/Combine/fit.png width 1280 height 517
> supersample 3
> hide #!6 models
> hide #!5 models
> show #!4 models
> hide #!4 models
> show #4 cartoons
> show #4 cartoons
> show #!5 models
> show #!4 models
> show #4 cartoons
> hide #4
> show #4
> hide #4
> show #4 cartoons
> hide #!3 models
> show #!3 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> hide #!1 models
> hide #!4 models
> show #!4 models
> hide #4.1 models
> show #4.1 models
> hide #!4 models
> show #!4 models
> cartoon
> select #4
92764 atoms, 94889 bonds, 88 pseudobonds, 2 models selected
> show sel cartoons
> show sel cartoons
> show sel atoms
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> show sel cartoons
> hide sel atoms
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting full
> toolshed show "Side View"
> close #4
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #!1 models
> show #!2 models
> show #!3 models
> show #!5 models
> show #!6 models
> view DEF
> save2 /Users/SYC/Desktop/Lig/Synaptic_Complex.cxs
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 564, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e30ef10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x16de49790> 'Ku1.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'Ku1.pdb'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 276, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 1263, in take_snapshot
'structure state': Structure.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/structure.py", line 152, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 324, in take_snapshot
'positions': self.positions.array(),
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1373, in <lambda>
action.triggered.connect(lambda arg, cb = callback: cb())
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 90, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 101, in show_save_file_dialog
_dlg.display(session, session.ui.main_window)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 31, in display
run(session, cmd)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run
results = command.run(text, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 60, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2848, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 73, in provider_save
mgr).save(session, path, **provider_kw)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core_formats/__init__.py", line 79, in save
return cxs_save(session, path, **kw)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 811, in save
session.save(output, version=version, include_maps=include_maps)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 564, in save
mgr.discovery(self._state_containers)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 255, in discovery
self.processed[key] = self.process(obj, parents)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'nucleotides' ->
<chimerax.atomic.nucleotides._data.NucleotideState object at 0x12e30ef10> ->
<chimerax.atomic.structure.AtomicStructure object at 0x16de49790> 'Ku1.pdb'
RuntimeError: Error while saving session data for 'nucleotides' -> ->
'Ku1.pdb'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 279, in process
raise RuntimeError(msg) from e
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-10.36.32
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Nucleotides: asking for distance from None |
| Version: | → 0.93 |
comment:2 by , 5 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
This was fixed shortly have 0.93 was released. The bug is part of #3057. Please upgrade your version of ChimeraX.