Error reading pbonds file

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.0 (2020-06-04 23:15:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.0 (2020-06-04)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/Fabian/Downloads/AF-P54819-F1-model_v3.pdb

AF-P54819-F1-model_v3.pdb title:  
Alphafold monomer V2.0 prediction for adenylate kinase 2, mitochondrial
(P54819) [more info...]  
  
Chain information for AF-P54819-F1-model_v3.pdb #1  
---  
Chain | Description  
A | adenylate kinase 2, mitochondrial  
  

> set bgColor white

> select /A:209

5 atoms, 4 bonds, 1 model selected  

> select up

37 atoms, 37 bonds, 1 model selected  

> select up

1854 atoms, 1888 bonds, 1 model selected  

> color sel red

> color sel light blue

> select clear

> color bfactor

1854 atoms, 239 residues, atom bfactor range 38.4 to 98.3  
Alignment identifier is 1.A  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> color byhetero

> mlp

Map values for surface "AF-P54819-F1-model_v3.pdb_A SES surface": minimum
-28.82, mean -4.691, maximum 21.55  

> color bfactor

1854 atoms, 239 residues, 1 surfaces, atom bfactor range 38.4 to 98.3  

> rainbow

> color bychain

> color bychain

> color byhetero

> color bychain

> color sel light blue

> hide surfaces

> color sel light blue

> select /A:219

7 atoms, 6 bonds, 1 model selected  

> select up

146 atoms, 148 bonds, 2 models selected  

> select up

1854 atoms, 1888 bonds, 2 models selected  

> color sel light blue

> color sel light blue

> select clear

> lighting flat

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting shadows false

> lighting shadows true

> lighting flat

> lighting full

> lighting flat

> save C:\Users\Fabian\Desktop\image45.png supersample 3

> save C:\Users\Fabian\Desktop\image46.png supersample 3

> color sel lightblue red

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color sel red

> select clear

> color sel red

> select clear

> save C:\Users\Fabian\Desktop\image47.png supersample 3

> open C:/Users/Fabian/Downloads/7ajb.cif

7ajb.cif title:  
bovine ATP synthase dimer state1:state1 [more info...]  
  
Chain information for 7ajb.cif #2  
---  
Chain | Description  
8 A8 | ATP synthase protein 8  
A AA AB AC B C | ATP synthase subunit alpha, mitochondrial  
AD AE AF D E F | ATP synthase subunit beta, mitochondrial  
AG G | ATP synthase subunit gamma, mitochondrial  
AH H | ATP synthase subunit delta, mitochondrial  
AI I | ATP synthase subunit epsilon, mitochondrial  
AJ J | ATPase inhibitor, mitochondrial  
AK AL AM AN AO AP AQ AR K L M N O P Q R | ATP synthase F(0) complex subunit
C2, mitochondrial  
AS S | ATP synthase subunit O, mitochondrial  
Aa a | ATP synthase subunit a  
Ab b | ATP synthase F(0) complex subunit B1, mitochondrial  
Ad d | ATP synthase subunit d, mitochondrial  
Ae e | ATP synthase subunit e, mitochondrial  
Af f | ATP synthase subunit f, mitochondrial  
Ag g | ATP synthase subunit g, mitochondrial  
Ah h | ATP synthase-coupling factor 6, mitochondrial  
Aj j | ATP synthase subunit ATP5MPL, mitochondrial  
Ak k | ATP synthase membrane subunit DAPIT, mitochondrial  
  
Non-standard residues in 7ajb.cif #2  
---  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
  

> hide #!1 models

> select #2/AB:154@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

40 atoms, 39 bonds, 1 model selected  

> select up

2339 atoms, 2337 bonds, 1 model selected  

> select up

51424 atoms, 51352 bonds, 1 model selected  

> select down

2339 atoms, 2337 bonds, 1 model selected  

> select up

51424 atoms, 51352 bonds, 1 model selected  

> select down

2339 atoms, 2337 bonds, 1 model selected  

> hide #2.1 models

> show #2.1 models

> hide

> undo

> hide sel cartoons

> hide sel atoms

> select #2/AF:201@O

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

74 atoms, 73 bonds, 1 model selected  

> select up

2290 atoms, 2289 bonds, 1 model selected  

> hide sel atoms

> select #2/AC:273@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

80 atoms, 79 bonds, 1 model selected  

> select up

2443 atoms, 2441 bonds, 1 model selected  

> hide sel atoms

> select #2/AE:119@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

104 atoms, 103 bonds, 1 model selected  

> select up

2290 atoms, 2289 bonds, 1 model selected  

> hide sel atoms

> select #2/AA:370@O

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

68 atoms, 67 bonds, 1 model selected  

> select up

2491 atoms, 2490 bonds, 1 model selected  

> hide sel atoms

> select #2/AG:92@N

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

95 atoms, 94 bonds, 1 model selected  

> select up

1347 atoms, 1346 bonds, 1 model selected  

> hide sel atoms

> select #2/AK:25@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

113 atoms, 112 bonds, 1 model selected  

> hide sel atoms

> select #2/AR:36@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

108 atoms, 107 bonds, 1 model selected  

> select up

364 atoms, 363 bonds, 1 model selected  

> select up

51424 atoms, 51352 bonds, 1 model selected  

> select down

364 atoms, 363 bonds, 1 model selected  

> hide sel atoms

> select #2/AH:93@N

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

25 atoms, 24 bonds, 1 model selected  

> select up

653 atoms, 652 bonds, 1 model selected  

> hide sel atoms

> select #2/AI:15@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

75 atoms, 74 bonds, 1 model selected  

> select up

233 atoms, 232 bonds, 1 model selected  

> hide sel atoms

> select #2/AS:49@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

45 atoms, 44 bonds, 1 model selected  

> select up

931 atoms, 930 bonds, 1 model selected  

> hide sel atoms

> select #2/Ad:94@N

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

65 atoms, 64 bonds, 1 model selected  

> select up

778 atoms, 777 bonds, 1 model selected  

> hide sel atoms

> select #2/Aj:29@CA

1 atom, 1 model selected  

> select up

4 atoms, 3 bonds, 1 model selected  

> select up

138 atoms, 137 bonds, 1 model selected  

> select up

238 atoms, 237 bonds, 1 model selected  

> hide sel atoms

> select #2/AD:15@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

34 atoms, 33 bonds, 1 model selected  

> select up

2300 atoms, 2299 bonds, 1 model selected  

> hide sel atoms

> select #2/AJ:18@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

29 atoms, 28 bonds, 1 model selected  

> select up

231 atoms, 230 bonds, 1 model selected  

> hide sel atoms

> select #2/Ah:21@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

90 atoms, 89 bonds, 1 model selected  

> select up

306 atoms, 305 bonds, 1 model selected  

> hide sel atoms

> select #2/Ab:143@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

320 atoms, 319 bonds, 1 model selected  

> select up

1035 atoms, 1034 bonds, 1 model selected  

> hide sel atoms

> select #2/AQ:50@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

153 atoms, 152 bonds, 1 model selected  

> hide sel atoms

> select #2/AO:6@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

68 atoms, 67 bonds, 1 model selected  

> select up

364 atoms, 363 bonds, 1 model selected  

> hide sel atoms

> select #2/Ak:13@CA

1 atom, 1 model selected  

> select up

4 atoms, 3 bonds, 1 model selected  

> select up

29 atoms, 28 bonds, 1 model selected  

> select up

177 atoms, 176 bonds, 1 model selected  

> hide sel atoms

> select #2/Aa:132@C

1 atom, 1 model selected  

> select up

4 atoms, 3 bonds, 1 model selected  

> select up

29 atoms, 28 bonds, 1 model selected  

> select up

1203 atoms, 1201 bonds, 1 model selected  

> hide sel atoms

> select #2/A8:35@N

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

55 atoms, 54 bonds, 1 model selected  

> select up

205 atoms, 204 bonds, 1 model selected  

> hide sel atoms

> select #2/Af:49@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

102 atoms, 101 bonds, 1 model selected  

> select up

658 atoms, 653 bonds, 1 model selected  

> hide sel atoms

> select #2/Ag:81@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

132 atoms, 131 bonds, 1 model selected  

> select up

390 atoms, 389 bonds, 1 model selected  

> hide sel atoms

> select #2/Ae:18@N

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

252 atoms, 251 bonds, 1 model selected  

> select up

277 atoms, 276 bonds, 1 model selected  

> hide sel atoms

> select clear

> select up

Nothing selected  

> select up

Nothing selected  

> select up

Nothing selected  

> select #2/AL:56@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

143 atoms, 142 bonds, 1 model selected  

> select up

359 atoms, 358 bonds, 1 model selected  

> hide sel atoms

> select #2/AQ:7@O

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

68 atoms, 67 bonds, 1 model selected  

> select up

364 atoms, 363 bonds, 1 model selected  

> hide sel atoms

> select #2/AP:33@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

98 atoms, 97 bonds, 1 model selected  

> select up

359 atoms, 358 bonds, 1 model selected  

> select #2/AM:38@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

104 atoms, 103 bonds, 1 model selected  

> select up

364 atoms, 363 bonds, 1 model selected  

> hide sel atoms

> select #2/AN:16@O

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

9 atoms, 8 bonds, 1 model selected  

> select up

364 atoms, 363 bonds, 1 model selected  

> hide sel atoms

> select #2/AK:54@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

143 atoms, 142 bonds, 1 model selected  

> select up

359 atoms, 358 bonds, 1 model selected  

> hide sel atoms

> select #2/AP:34@N

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

98 atoms, 97 bonds, 1 model selected  

> select up

359 atoms, 358 bonds, 1 model selected  

> hide sel atoms

> open C:/Users/Fabian/Downloads/SRCH=17592--ChimeraX--
> MAN.LINEARS.MONOLINKS.XLINKS.BTWN.SELF.HOMOM.NOTHOMOMULT.AMBIG.PEPLEN=1.A.B.C.Q.DECOYS.TARGETS.DISTUNK.MGRP.URPPPI=1.MATCHSCORES=0-35.GROUPS=NA.pb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 382, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\\__init__.py", line 25, in open  
return readpbonds.read_pseudobond_file(session, data, file_name)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 52, in read_pseudobond_file  
% (i, len(a), aspec))  
File "<string>", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1/d:62@CA", require exactly 1  
  
File "", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1/d:62@CA", require exactly 1  
  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 52, in read_pseudobond_file  
% (i, len(a), aspec))  
  
See log for complete Python traceback.  
  

> show cartoons

> select #2/C:377@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 1 model selected  

> select up

97 atoms, 96 bonds, 1 model selected  

> select up

2443 atoms, 2441 bonds, 1 model selected  

> select up

51424 atoms, 51352 bonds, 1 model selected  

> select up

53278 atoms, 53240 bonds, 2 models selected  

> show cartoons

> show cartoons

> hide sel & #!2 atoms

> select clear

> style pbonds dashes 0Changed 2 pseduobond dashes

Invalid "dashes" argument: Expected an integer  

> open C:/Users/Fabian/Downloads/SRCH=17592--ChimeraX--
> MAN.LINEARS.MONOLINKS.XLINKS.BTWN.SELF.HOMOM.NOTHOMOMULT.AMBIG.PEPLEN=1.A.B.C.Q.DECOYS.TARGETS.DISTUNK.MGRP.URPPPI=1.MATCHSCORES=0-35.GROUPS=NA.pb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 382, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\\__init__.py", line 25, in open  
return readpbonds.read_pseudobond_file(session, data, file_name)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 52, in read_pseudobond_file  
% (i, len(a), aspec))  
File "<string>", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1/d:62@CA", require exactly 1  
  
File "", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1/d:62@CA", require exactly 1  
  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 52, in read_pseudobond_file  
% (i, len(a), aspec))  
  
See log for complete Python traceback.  
  

> hide #!2 models

> hide #2.1 models

> open C:/Users/Fabian/Downloads/SRCH=17592--ChimeraX--
> MAN.LINEARS.MONOLINKS.XLINKS.BTWN.SELF.HOMOM.NOTHOMOMULT.AMBIG.PEPLEN=1.A.B.C.Q.DECOYS.TARGETS.DISTUNK.MGRP.URPPPI=1.MATCHSCORES=0-35.GROUPS=NA(1).pb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\dialog.py", line 150, in _qt_safe  
if data_format is None else " format " +
StringArg.unparse(data_format.nicknames[0])))  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 101, in cmd_open  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 152, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 382, in collated_open  
return func(*func_args, **func_kw)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\\__init__.py", line 25, in open  
return readpbonds.read_pseudobond_file(session, data, file_name)  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 52, in read_pseudobond_file  
% (i, len(a), aspec))  
File "<string>", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1/d:62@CA", require exactly 1  
  
File "", line None  
SyntaxError: Line 0, got 0 atoms for spec "#1/d:62@CA", require exactly 1  
  
File "C:\Program Files\ChimeraX 1.0\bin\lib\site-
packages\chimerax\read_pbonds\readpbonds.py", line 52, in read_pseudobond_file  
% (i, len(a), aspec))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 30.0.101.1122
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 10SQCTO1WW
OS: Microsoft Windows 10 Pro (Build 18363)
Memory: 8,454,348,800
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8

[Eric Pettersen]

This was changed into a UserError awhile ago.