Opened 6 years ago

Closed 6 years ago

#2370 closed defect (can't reproduce)

(atomic) model: self.positions is None

Reported by: sitins07@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Greg Couch
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.17763
ChimeraX Version: 0.91 (2019-08-30)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-08-30)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4v95

4v95 title:  
Crystal structure of YAEJ bound to the 70S ribosome [more info...]  
  
Chain information for 4v95 #1  
---  
Chain | Description  
AA CA | 16S Ribosomal RNA  
AB CB | 30S Ribosomal Protein S2  
AC CC | 30S Ribosomal Protein S3  
AD CD | 30S Ribosomal Protein S4  
AE CE | 30S Ribosomal Protein S5  
AF CF | 30S Ribosomal Protein S6  
AG CG | 30S Ribosomal Protein S7  
AH CH | 30S Ribosomal Protein S8  
AI CI | 30S Ribosomal Protein S9  
AJ CJ | 30S Ribosomal Protein S10  
AK CK | 30S Ribosomal Protein S11  
AL CL | 30S Ribosomal Protein S12  
AM CM | 30S Ribosomal Protein S13  
AN CN | 30S Ribosomal Protein S14  
AO CO | 30S Ribosomal Protein S15  
AP CP | 30S Ribosomal Protein S16  
AQ CQ | 30S Ribosomal Protein S17  
AR CR | 30S Ribosomal Protein S18  
AS CS | 30S Ribosomal Protein S19  
AT CT | 30S Ribosomal Protein S20  
AU CU | 30S Ribosomal Protein THX  
AV CV | P-site fMet-tRNA  
AX CX | mRNA  
AY | YAEJ  
B0 D0 | 50S Ribosomal Protein L27  
B1 D1 | 50S Ribosomal Protein L28  
B2 D2 | 50S Ribosomal Protein L29  
B3 D3 | 50S Ribosomal Protein L30  
B4 D4 | 50S Ribosomal Protein L31  
B5 D5 | 50S Ribosomal Protein L32  
B6 D6 | 50S Ribosomal Protein L33  
B7 D7 | 50S Ribosomal Protein L34  
B8 D8 | 50S Ribosomal Protein L35  
B9 D9 | 50S Ribosomal Protein L36  
BA DA | 23S Ribosomal RNA  
BB DB | 5S Ribosomal RNA  
BD DD | 50S Ribosomal Protein L2  
BE DE | 50S Ribosomal Protein L3  
BF DF | 50S Ribosomal Protein L4  
BG DG | 50S Ribosomal Protein L5  
BH DH | 50S Ribosomal Protein L6  
BI DI | 50S Ribosomal Protein L9  
BN DN | 50S Ribosomal Protein L13  
BO DO | 50S Ribosomal Protein L14  
BP DP | 50S Ribosomal Protein L15  
BQ DQ | 50S Ribosomal Protein L16  
BR DR | 50S Ribosomal Protein L17  
BS DS | 50S Ribosomal Protein L18  
BT DT | 50S Ribosomal Protein L19  
BU DU | 50S Ribosomal Protein L20  
BV DV | 50S Ribosomal Protein L21  
BW DW | 50S Ribosomal Protein L22  
BX DX | 50S Ribosomal Protein L23  
BY DY | 50S Ribosomal Protein L24  
BZ DZ | 50S Ribosomal Protein L25  
  
Non-standard residues in 4v95 #1  
---  
MG — magnesium ion  
ZN — zinc ion  
  
4v95 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  
  

> open Z:/ALL/Niels/Valik/For_Poster/4v95_phases_2mFo-DFc.ccp4

Opened 4v95_phases_2mFo-DFc.ccp4, grid size 398,450,568, pixel
0.778,0.779,0.78, shown at level 0.562, step 2, values float32  

> cd Z:/ALL/Niels/Valik/For_Poster/

Current working directory is: Z:\ALL\Niels\Valik\For_Poster  

> save 4v95.pdb models #1

> close #2

> close #1

> open Z:/ALL/Niels/Valik/For_Poster/X-ray.mrc
Z:/ALL/Niels/Valik/For_Poster/4v95_70SArfB.pdb

Summary of feedback from opening files  
---  
warnings | Ignored bad PDB record found on line 148062  
END  
  
CONECT record to nonexistent atom: (363, 31840)  
CONECT record to nonexistent atom: (949, 31552)  
CONECT record to nonexistent atom: (1056, 31567)  
CONECT record to nonexistent atom: (1874, 31592)  
CONECT record to nonexistent atom: (1874, 31593)  
201 messages similar to the above omitted  
CONECT record for nonexistent atom: 31515  
Bad residue range for secondary structure: HELIX 24 24 ASN A 199 ARG A 209 1
11  
Bad residue range for secondary structure: HELIX 28 28 ASN A 127 ARG A 140 1
14  
Bad residue range for secondary structure: HELIX 39 39 ASP A 4 ARG A 18 1 15  
Bad residue range for secondary structure: HELIX 40 40 SER A 29 GLU A 42 1 14  
Bad residue range for secondary structure: HELIX 45 45 GLU A 48 VAL A 53 1 6  
45 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 160 160 ASN C 25 ARG C
30 1 6  
Start residue of secondary structure not found: HELIX 161 161 ASP C 43 MET C
63 1 21  
Start residue of secondary structure not found: HELIX 162 162 LYS C 74 GLY C
89 1 16  
Start residue of secondary structure not found: HELIX 163 163 ASN C 104 GLU C
116 1 13  
Start residue of secondary structure not found: HELIX 164 164 LYS C 132 ARG C
153 1 22  
153 messages similar to the above omitted  
Bad residue range for secondary structure: SHEET 22 22 1 VAL A 41 ALA A 48 0  
Bad residue range for secondary structure: SHEET 28 28 1 ARG A 2 LEU A 10 0  
Bad residue range for secondary structure: SHEET 37 37 1 TYR A 85 MET A 89 0  
Bad residue range for secondary structure: SHEET 39 39 1 ILE A 45 GLU A 49 0  
Bad residue range for secondary structure: SHEET 41 41 1 HIS A 82 ARG A 85 0  
61 messages similar to the above omitted  
Start residue of secondary structure not found: SHEET 256 256 1 ILE C 32 ARG C
36 0  
Start residue of secondary structure not found: SHEET 257 257 1 ILE C 39 ILE C
42 0  
Start residue of secondary structure not found: SHEET 258 258 1 PHE C 70 VAL C
71 0  
Start residue of secondary structure not found: SHEET 259 259 1 TYR C 92 VAL C
93 0  
Start residue of secondary structure not found: SHEET 260 260 1 ILE C 162 VAL
C 164 0  
243 messages similar to the above omitted  
  
Opened X-ray.mrc, grid size 398,450,568, pixel 0.778,0.779,0.78, shown at
level 0.562, step 2, values float32  
  
Chain information for 4v95_70SArfB.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/A | No description available  
1.2/B | No description available  
1.2/B | No description available  
  

> open Z:/ALL/Niels/Valik/For_Poster/Model_3_major_state_Mg-
wz.Q28-coot-0_Niels.pdb

Summary of feedback from opening
Z:/ALL/Niels/Valik/For_Poster/Model_3_major_state_Mg-wz.Q28-coot-0_Niels.pdb  
---  
warning | Ignored bad PDB record found on line 147722  
END  
  
Chain information for Model_3_major_state_Mg-wz.Q28-coot-0_Niels.pdb #2  
---  
Chain | Description  
0 | No description available  
1 | No description available  
2 | No description available  
3 | No description available  
4 | No description available  
5 | No description available  
6 | No description available  
A | No description available  
B | No description available  
C | 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  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | 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  
j | No description available  
k | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
w | No description available  
x | No description available  
y | No description available  
z | No description available  
  

> open Z:/ALL/Niels/Valik/For_Poster/X-ray_resampled.mrc

Opened X-ray_resampled.mrc, grid size 512,512,512, pixel 0.652, shown at level
0.481, step 2, values float32  

> hide #!2 models

> select #1.2/A:104

108 atoms, 99 bonds, 1 model selected  

> select up

40236 atoms, 44299 bonds, 1 model selected  

> select down

108 atoms, 99 bonds, 1 model selected  

> open Z:/ALL/Niels/Valik/For_Poster/4v95.cif

4v95.cif title:  
Crystal structure of YAEJ bound to the 70S ribosome [more info...]  
  
Chain information for 4v95.cif #4  
---  
Chain | Description  
AA CA | 16S Ribosomal RNA  
AB CB | 30S Ribosomal Protein S2  
AC CC | 30S Ribosomal Protein S3  
AD CD | 30S Ribosomal Protein S4  
AE CE | 30S Ribosomal Protein S5  
AF CF | 30S Ribosomal Protein S6  
AG CG | 30S Ribosomal Protein S7  
AH CH | 30S Ribosomal Protein S8  
AI CI | 30S Ribosomal Protein S9  
AJ CJ | 30S Ribosomal Protein S10  
AK CK | 30S Ribosomal Protein S11  
AL CL | 30S Ribosomal Protein S12  
AM CM | 30S Ribosomal Protein S13  
AN CN | 30S Ribosomal Protein S14  
AO CO | 30S Ribosomal Protein S15  
AP CP | 30S Ribosomal Protein S16  
AQ CQ | 30S Ribosomal Protein S17  
AR CR | 30S Ribosomal Protein S18  
AS CS | 30S Ribosomal Protein S19  
AT CT | 30S Ribosomal Protein S20  
AU CU | 30S Ribosomal Protein THX  
AV CV | P-site fMet-tRNA  
AX CX | mRNA  
AY | YAEJ  
B0 D0 | 50S Ribosomal Protein L27  
B1 D1 | 50S Ribosomal Protein L28  
B2 D2 | 50S Ribosomal Protein L29  
B3 D3 | 50S Ribosomal Protein L30  
B4 D4 | 50S Ribosomal Protein L31  
B5 D5 | 50S Ribosomal Protein L32  
B6 D6 | 50S Ribosomal Protein L33  
B7 D7 | 50S Ribosomal Protein L34  
B8 D8 | 50S Ribosomal Protein L35  
B9 D9 | 50S Ribosomal Protein L36  
BA DA | 23S Ribosomal RNA  
BB DB | 5S Ribosomal RNA  
BD DD | 50S Ribosomal Protein L2  
BE DE | 50S Ribosomal Protein L3  
BF DF | 50S Ribosomal Protein L4  
BG DG | 50S Ribosomal Protein L5  
BH DH | 50S Ribosomal Protein L6  
BI DI | 50S Ribosomal Protein L9  
BN DN | 50S Ribosomal Protein L13  
BO DO | 50S Ribosomal Protein L14  
BP DP | 50S Ribosomal Protein L15  
BQ DQ | 50S Ribosomal Protein L16  
BR DR | 50S Ribosomal Protein L17  
BS DS | 50S Ribosomal Protein L18  
BT DT | 50S Ribosomal Protein L19  
BU DU | 50S Ribosomal Protein L20  
BV DV | 50S Ribosomal Protein L21  
BW DW | 50S Ribosomal Protein L22  
BX DX | 50S Ribosomal Protein L23  
BY DY | 50S Ribosomal Protein L24  
BZ DZ | 50S Ribosomal Protein L25  
  
Non-standard residues in 4v95.cif #4  
---  
MG — magnesium ion  
ZN — zinc ion  
  
4v95.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> close #4

> open Z:/ALL/Niels/Valik/For_Poster/4v95.cif

4v95.cif title:  
Crystal structure of YAEJ bound to the 70S ribosome [more info...]  
  
Chain information for 4v95.cif #4  
---  
Chain | Description  
AA CA | 16S Ribosomal RNA  
AB CB | 30S Ribosomal Protein S2  
AC CC | 30S Ribosomal Protein S3  
AD CD | 30S Ribosomal Protein S4  
AE CE | 30S Ribosomal Protein S5  
AF CF | 30S Ribosomal Protein S6  
AG CG | 30S Ribosomal Protein S7  
AH CH | 30S Ribosomal Protein S8  
AI CI | 30S Ribosomal Protein S9  
AJ CJ | 30S Ribosomal Protein S10  
AK CK | 30S Ribosomal Protein S11  
AL CL | 30S Ribosomal Protein S12  
AM CM | 30S Ribosomal Protein S13  
AN CN | 30S Ribosomal Protein S14  
AO CO | 30S Ribosomal Protein S15  
AP CP | 30S Ribosomal Protein S16  
AQ CQ | 30S Ribosomal Protein S17  
AR CR | 30S Ribosomal Protein S18  
AS CS | 30S Ribosomal Protein S19  
AT CT | 30S Ribosomal Protein S20  
AU CU | 30S Ribosomal Protein THX  
AV CV | P-site fMet-tRNA  
AX CX | mRNA  
AY | YAEJ  
B0 D0 | 50S Ribosomal Protein L27  
B1 D1 | 50S Ribosomal Protein L28  
B2 D2 | 50S Ribosomal Protein L29  
B3 D3 | 50S Ribosomal Protein L30  
B4 D4 | 50S Ribosomal Protein L31  
B5 D5 | 50S Ribosomal Protein L32  
B6 D6 | 50S Ribosomal Protein L33  
B7 D7 | 50S Ribosomal Protein L34  
B8 D8 | 50S Ribosomal Protein L35  
B9 D9 | 50S Ribosomal Protein L36  
BA DA | 23S Ribosomal RNA  
BB DB | 5S Ribosomal RNA  
BD DD | 50S Ribosomal Protein L2  
BE DE | 50S Ribosomal Protein L3  
BF DF | 50S Ribosomal Protein L4  
BG DG | 50S Ribosomal Protein L5  
BH DH | 50S Ribosomal Protein L6  
BI DI | 50S Ribosomal Protein L9  
BN DN | 50S Ribosomal Protein L13  
BO DO | 50S Ribosomal Protein L14  
BP DP | 50S Ribosomal Protein L15  
BQ DQ | 50S Ribosomal Protein L16  
BR DR | 50S Ribosomal Protein L17  
BS DS | 50S Ribosomal Protein L18  
BT DT | 50S Ribosomal Protein L19  
BU DU | 50S Ribosomal Protein L20  
BV DV | 50S Ribosomal Protein L21  
BW DW | 50S Ribosomal Protein L22  
BX DX | 50S Ribosomal Protein L23  
BY DY | 50S Ribosomal Protein L24  
BZ DZ | 50S Ribosomal Protein L25  
  
Non-standard residues in 4v95.cif #4  
---  
MG — magnesium ion  
ZN — zinc ion  
  
4v95.cif mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> mmaker #4/AY to #2/y

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 Model_3_major_state_Mg-wz.Q28-coot-0_Niels.pdb, chain y (#2) with
4v95.cif, chain AY (#4), sequence alignment score = 634.5  
RMSD between 82 pruned atom pairs is 0.762 angstroms; (across all 132 pairs:
2.902)  
  

> select #4

284877 atoms, 303230 bonds, 14000 pseudobonds, 4 models selected  

> style sel stick

Changed 284877 atom styles  

> hide sel atoms

> select #1.2

140349 atoms, 152485 bonds, 10 pseudobonds, 3 models selected  

> hide sel cartoons

> hide sel atoms

> select #4/y

Nothing selected  

> select #4/AY

1034 atoms, 1043 bonds, 1 model selected  

> show sel atoms

> color zone #3 near sel distance 2 sharpEdges true

> volume splitbyzone #3

> save session Z:/ALL/Niels/Valik/For_Poster/X-ray.cxs

> save session Z:/ALL/Niels/Valik/For_Poster/X-ray.cxs includeMaps true

> view sel

> save session Z:/ALL/Niels/Valik/For_Poster/X-ray.cxs includeMaps true

> close #1.2

> close #1

> show #!2 models

> select #2

147646 atoms, 159894 bonds, 1 model selected  

> style sel stick

Changed 147646 atom styles  

> hide sel atoms

> hide sel cartoons

> select #2/y

1047 atoms, 1059 bonds, 1 model selected  

> show sel atoms

> open Z:/ALL/Niels/Valik/For_Poster/Volumes/gs/gs_arfb.mrc

Opened gs_arfb.mrc, grid size 512,512,512, pixel 0.652, shown at level
0.00126, step 2, values float32  

> hide #!1 models

> hide #!4 models

> save session Z:/ALL/Niels/Valik/For_Poster/X-ray.cxs includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2394, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 164, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\models.py", line 275, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'NoneType' object has no
attribute 'array'  
  
RuntimeError: Error while saving session data for "": 'NoneType' object has no
attribute 'array'  
  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2394, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 164, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\models.py", line 275, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 84, in handle_scheme  
cmd(self.session)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 166, in _file_save  
session.ui.main_window.file_save_cb(session)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\ui\gui.py", line 601, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 138, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 1062, in save  
run(session, cmd)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 956, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\io.py", line 213, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'NoneType' object has no
attribute 'array'  
  
RuntimeError: Error while saving session data for "": 'NoneType' object has no
attribute 'array'  
  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  

> save session Z:/ALL/Niels/Valik/For_Poster/X-ray-1.cxs includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2394, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 164, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\models.py", line 275, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'NoneType' object has no
attribute 'array'  
  
RuntimeError: Error while saving session data for "": 'NoneType' object has no
attribute 'array'  
  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2394, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 164, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\models.py", line 275, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 84, in handle_scheme  
cmd(self.session)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 166, in _file_save  
session.ui.main_window.file_save_cb(session)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\ui\gui.py", line 601, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 138, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 1062, in save  
run(session, cmd)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 956, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\io.py", line 213, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'NoneType' object has no
attribute 'array'  
  
RuntimeError: Error while saving session data for "": 'NoneType' object has no
attribute 'array'  
  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  

> show #!3 models

> hide #!3 models

> close #3

> save session Z:/ALL/Niels/Valik/For_Poster/X-ray-1.cxs includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2394, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 164, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\models.py", line 275, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'NoneType' object has no
attribute 'array'  
  
RuntimeError: Error while saving session data for "": 'NoneType' object has no
attribute 'array'  
  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 255, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 2394, in take_snapshot  
'structure state': Structure.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\atomic\structure.py", line 164, in take_snapshot  
data = {'model state': Model.take_snapshot(self, session, flags),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\models.py", line 275, in take_snapshot  
'positions': self.positions.array(),  
AttributeError: 'NoneType' object has no attribute 'array'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 84, in handle_scheme  
cmd(self.session)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 166, in _file_save  
session.ui.main_window.file_save_cb(session)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\ui\gui.py", line 601, in file_save_cb  
self.save_dialog.display(self, session)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\ui\save_dialog.py", line 138, in display  
fmt.save(session, filename)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 1062, in save  
run(session, cmd)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 956, in save_session  
save(session, filename, **kw)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\commands\save.py", line 61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\io.py", line 213, in export  
result = self.export_func(session, path, **kw)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 769, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 532, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 234, in discovery  
self.processed[key] = self.process(obj)  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
RuntimeError: Error while saving session data for "<class
'chimerax.atomic.structure.AtomicStructure'>": 'NoneType' object has no
attribute 'array'  
  
RuntimeError: Error while saving session data for "": 'NoneType' object has no
attribute 'array'  
  
File "C:\Program Files\ChimeraX_01092019\bin\lib\site-
packages\chimerax\core\session.py", line 258, in process  
raise RuntimeError(msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 397.93
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Change History (5)

comment:1 by Eric Pettersen, 6 years ago

Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → (atomic) model: self.positions is None

comment:2 by Tom Goddard, 6 years ago

This ChimeraX error happened when saving a session. The error was because the session save attempted to save a closed atomic Structure. The same session save succeeded about 10 commands prior to this failed one. About 8 commands prior to the failed one there are commands "close #1.2" and "close #1". Model #1.2 was an atomic structure and I suspect it somehow did not get closed. A couple lines before the failed save is the command "hide #!1 models" most likely issued by clicking there show/hide button for model #1 in the model panel. But there should be no model #1 at this point because of the preceding "close #1". So the problem seems to be that the "close #1.2" and "close #1" deleted the models but left them in model panel and in the set of open models. I'm not sure how that can happen.

comment:3 by Tom Goddard, 6 years ago

Cc: Greg Couch added

The previous comment was wrong. The "close #1" probably worked. There was an MRC file opened that became #1 after that close.

But it does seem that the "close #1.2" that closes an atomic structure opened earlier is the model that session save is trying to save even though it has been deleted. This can happen if some ChimeraX tool is referring to that structure even though it has been closed. I don't see in the log any indication of what tool might be holding a reference to the deleted structure.

This kind of error where session saving fails and it is not apparent who was trying to save a deleted object has happened before and Greg Couch is supposed to improve the error reporting so the path to the object is output when an error occurs during save. We will probably have to wait for that improvement to go in, and another report of this bug to locate the problem.

comment:4 by Greg Couch, 6 years ago

Improvements to the error reporting when saving sessions is already in the daily build (as of today).

comment:5 by Tom Goddard, 6 years ago

Resolution: → can't reproduce
Status: assigned → closed

It appears some ChimeraX tool tried to save a closed model in the session. Greg's new error reporting should identify what tool is doing that if this error happens again. Without knowing that we won't be able to fix it. So I will close this ticket -- please report a new bug if you see it again.

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