Opened 4 years ago

Closed 4 years ago

#6564 closed defect (fixed)

Error when building single nucleotide

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-5.4.0-99-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted

Thread 0x00007f0462dd5740 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
> set bgColor white

> hide #!2 models

> show atoms

> hide cartoons

> nucleotides atoms

> style nucleic stick

Changed 1896 atom styles  

> select /C:72@O3'

1 atom, 1 residue, 1 model selected  

> select add /C:74@P

2 atoms, 2 residues, 1 model selected  

> ui tool show "Build Structure"

> bond sel reasonable false

Created 1 bond  

> select /C:24@O3'

1 atom, 1 residue, 1 model selected  

> select add /C:26@P

2 atoms, 2 residues, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> select /C:10@P

1 atom, 1 residue, 1 model selected  
FYI: command is replacing existing command: "build modify"  
FYI: command is replacing existing command: "build start"  
FYI: command is replacing existing command: "bond"  
FYI: command is replacing existing command: "~bond"  
FYI: command is replacing existing command: "bond length"  

> build modify /C:10@P O 0 resName N

Atom already has more bonds to heavy atoms than requested.  
Either delete some of those bonds/atoms or choose a different number of
requested bonds.  

> build modify /C:10@P O 2 geometry tetrahedral resName N

Atom already has more bonds to heavy atoms than requested.  
Either delete some of those bonds/atoms or choose a different number of
requested bonds.  

> build modify /C:10@P O 1 resName N

Atom already has more bonds to heavy atoms than requested.  
Either delete some of those bonds/atoms or choose a different number of
requested bonds.  

> build modify /C:10@P O 1 name O1 resName N

Atom already has more bonds to heavy atoms than requested.  
Either delete some of those bonds/atoms or choose a different number of
requested bonds.  

> select /C:46@OP3

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select /C:46@@serial_number=9344

1 atom, 1 residue, 1 model selected  

> select add /C:46@@serial_number=9371

2 atoms, 1 residue, 1 model selected  

> bond sel reasonable false

Created 1 bond  

> build start atom #1 res O

> delete atoms sel

> delete bonds sel

> addh

Summary of feedback from adding hydrogens to combined-phe-finished.pdb #1  
---  
warning | Not adding hydrogens to /C G 10 P because it is missing heavy-atom
bond partners  
notes | No usable SEQRES records for combined-phe-finished.pdb (#1) chain B;
guessing termini instead  
No usable SEQRES records for combined-phe-finished.pdb (#1) chain C; guessing
termini instead  
Chain-initial residues that are actual N termini: /B ASP 60  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /B ASN 578  
569 hydrogen bonds  
/B ASN 578 is not terminus, removing H atom from 'C'  
549 hydrogens added  
  

> select /C:10@P

1 atom, 1 residue, 1 model selected  

> select /C:10@P

1 atom, 1 residue, 1 model selected  

> build start nucleic #1 A type rna form B

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 113, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 113, in   
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/tool.py", line 386, in   
apply_but.clicked.connect(lambda checked: self._ss_apply_cb())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/tool.py", line 547, in _ss_apply_cb  
run(self.session, " ".join(["build start", provider_name, struct_arg,
subcmd_string]))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/cmd.py", line 51, in cmd_start_structure  
ret_val = manager.execute_command(method, model, subargs)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/manager.py", line 63, in execute_command  
return self._get_provider(name).execute_command(structure, args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/providers.py", line 272, in execute_command  
return cmd.run(self.name + ' ' + args, log=False)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/providers.py", line 539, in
shim_place_nucleic_acid  
chains = place_nucleic_acid(_structure, sequence, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/start.py", line 253, in place_nucleic_acid  
chains = Chains([residues1[0].chain, residues2[0].chain])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 1422, in __init__  
Collection.__init__(self, chain_pointers, molobject.Chain, Chains)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 118, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type ""  
  
ValueError: Collection items of unrecognized type ""  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 118, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  

> build start nucleic "custom built" A type rna form B

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 113, in __init__  
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 113, in   
pointers = numpy.array([i._c_pointer.value for i in items], cptr)  
AttributeError: 'NoneType' object has no attribute '_c_pointer'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/tool.py", line 386, in   
apply_but.clicked.connect(lambda checked: self._ss_apply_cb())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/tool.py", line 547, in _ss_apply_cb  
run(self.session, " ".join(["build start", provider_name, struct_arg,
subcmd_string]))  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/cmd.py", line 51, in cmd_start_structure  
ret_val = manager.execute_command(method, model, subargs)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/manager.py", line 63, in execute_command  
return self._get_provider(name).execute_command(structure, args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/providers.py", line 272, in execute_command  
return cmd.run(self.name + ' ' + args, log=False)[0]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/providers.py", line 539, in
shim_place_nucleic_acid  
chains = place_nucleic_acid(_structure, sequence, **kw)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/build_structure/start.py", line 253, in place_nucleic_acid  
chains = Chains([residues1[0].chain, residues2[0].chain])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 1422, in __init__  
Collection.__init__(self, chain_pointers, molobject.Chain, Chains)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 118, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
ValueError: Collection items of unrecognized type ""  
  
ValueError: Collection items of unrecognized type ""  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/atomic/molarray.py", line 118, in __init__  
raise ValueError('Collection items of unrecognized type "%s"' % t)  
  
See log for complete Python traceback.  
  

> build start nucleic "custom built" AC type rna form B

Chain information for custom built #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select #3

79 atoms, 87 bonds, 4 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,1.3318,0,1,0,-3.1749,0,0,1,-7.428

> view matrix models #3,1,0,0,3.567,0,1,0,0.76861,0,0,1,-5.5896

> ~select #3

Nothing selected  

> hide #3 models

> show #3 models

> select #3

79 atoms, 87 bonds, 4 residues, 1 model selected  

> view matrix models #3,1,0,0,-8.7527,0,1,0,9.8605,0,0,1,-11.771

> view matrix models #3,1,0,0,-3.4874,0,1,0,9.0617,0,0,1,-16.379

> view matrix models #3,1,0,0,-0.16069,0,1,0,9.4862,0,0,1,-14.542

> view matrix models #3,1,0,0,-0.56548,0,1,0,10.132,0,0,1,-12.617

> view matrix models #3,1,0,0,0.26255,0,1,0,11.906,0,0,1,-14.538

> view matrix models #3,1,0,0,-0.41667,0,1,0,12.563,0,0,1,-13.217

> view matrix models #3,1,0,0,-0.44801,0,1,0,12.809,0,0,1,-13.811

> view matrix models #3,1,0,0,-0.55928,0,1,0,12.966,0,0,1,-13.486

> select #3/A:2@OP2

1 atom, 1 residue, 1 model selected  

> select ~sel

10726 atoms, 10994 bonds, 1 pseudobond, 601 residues, 5 models selected  

> ~select #1

78 atoms, 87 bonds, 4 residues, 3 models selected  

> ~select #2

78 atoms, 87 bonds, 4 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #3/A:2@OP2

1 atom, 1 residue, 1 model selected  

> combine #1 #3

Remapping chain ID 'A' in custom built #3 to 'F'  

> hide #3 models

> ~select #3

Nothing selected  

> select #4/F:2@OP2

1 atom, 1 residue, 1 model selected  

> select add #1/C:10@P

2 atoms, 2 residues, 2 models selected  

> bond sel reasonable false

Cannot bond atoms in different molecules  

> hide #!1 models

> select #1

10648 atoms, 10907 bonds, 1 pseudobond, 597 residues, 2 models selected  

> ~select #1

Nothing selected  

> select #4/F:2@OP2

1 atom, 1 residue, 1 model selected  

> select add #4/C:10@P

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> select #4/A:1@HC

1 atom, 1 residue, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #4/C:77@O3'

1 atom, 1 residue, 1 model selected  

> select add #4/A:1@C

2 atoms, 2 residues, 1 model selected  

> bond sel

Created 1 bond  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to combined-phe-finished.pdb #1/C G 10 P
because it is missing heavy-atom bond partners  
Not adding hydrogens to custom built #3/A C 2 OP2 because it is missing heavy-
atom bond partners  
Not adding hydrogens to combination #4/C G 10 P because it is missing heavy-
atom bond partners  
Not adding hydrogens to combination #4/F C 2 OP2 because it is missing heavy-
atom bond partners  
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: combination #4/F C 2 OP2  
notes | No usable SEQRES records for combined-phe-finished.pdb (#1) chain B;
guessing termini instead  
No usable SEQRES records for combined-phe-finished.pdb (#1) chain C; guessing
termini instead  
Chain-initial residues that are actual N termini: combined-phe-finished.pdb
#1/B ASP 60  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combined-phe-finished.pdb
#1/B ASN 578  
561 hydrogen bonds  
combined-phe-finished.pdb #1/B ASN 578 is not terminus, removing H atom from
'C'  
No usable SEQRES records for custom built (#3) chain A; guessing termini
instead  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini:  
No usable SEQRES records for combination (#4) chain B; guessing termini
instead  
No usable SEQRES records for combination (#4) chain C; guessing termini
instead  
No usable SEQRES records for combination (#4) chain F; guessing termini
instead  
Chain-initial residues that are actual N termini: combination #4/B ASP 60  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: combination #4/B ASN 578  
561 hydrogen bonds  
combination #4/B ASN 578 is not terminus, removing H atom from 'C'  
50 hydrogens added  
  

> isolde start

> set selectionWidth 4

WARNING: no OpenCL or compatible CUDA drivers detected! While it is
theoretically possible to run ISOLDE using CPU only, in practice it is
prohibitively slow. If you have a suitable GPU in your machine, please check
that you have the recommended drivers from the manufacturer installed. The
current required CUDA version is 10.1 - if installed, please make sure this is
on your library path before starting ChimeraX.  

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
combined-phe-finished.pdb title:  
Alphafold monomer V2.0 prediction for GTP-binding protein 1 (O00178) [more
info...]  
  
Chain information for combined-phe-finished.pdb  
---  
Chain | Description  
1.2/B | No description available  
1.2/C | No description available  
  
Done loading forcefield  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Opened GTPBP1-tRNA-density.mrc as #4.1.1.1, grid size 400,400,400, pixel 1.16,
shown at step 1, values float32  

> select #4.2

10673 atoms, 10933 bonds, 1 pseudobond, 598 residues, 6 models selected  

> isolde sim start sel

ISOLDE: stopped sim  
Deleted the following atoms from residue G C46: OP1, C4', C5', C3', HN1, HN2,
O3', C2', O2', O4', C1', N9, C4, C5, N7, C8, N3, C2, HC6, HC1, HC2, HC, HC3,
P, HC4, OP1, HC5, O5', N2, N1, C6, O6, HN, OP2, HO  
Deleted the following atoms from residue G C1: OP1  
Deleted the following atoms from residue U C16: OP1  
Residue C F2 has only 1 atoms in common with the template. At least 3 are
needed to rebuild automatically. Adding of nucleic acid residues is not
currently possible in ISOLDE. To move forward, just delete this residue.  

> delete atoms (#!4.2 & sel)

> delete bonds (#!4.2 & sel)

> select #4.2

10637 atoms, 10893 bonds, 2 pseudobonds, 597 residues, 12 models selected  

> isolde sim start sel

Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  
ISOLDE: started sim  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open model-from-isolde-2.pdb

Summary of feedback from opening model-from-isolde-2.pdb  
---  
warning | Cannot find LINK/SSBOND residue A (77 )  
  
model-from-isolde-2.pdb title:  
Alphafold monomer V2.0 prediction for GTP-binding protein 1 (O00178) [more
info...]  
  
Chain information for model-from-isolde-2.pdb #1  
---  
Chain | Description  
B | No description available  
ii | No description available  
  
Non-standard residues in model-from-isolde-2.pdb #1  
---  
UNLJ — (UNLJ)  
  

> open GTPBP1-tRNA-density.mrc

Opened GTPBP1-tRNA-density.mrc as #2, grid size 400,400,400, pixel 1.16, shown
at level 1.8e-07, step 2, values float32  




OpenGL version: 3.3.0 NVIDIA 390.144
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision 7920 Tower
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 64 Intel(R) Xeon(R) Gold 6130 CPU @ 2.10GHz
Cache Size: 22528 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          187Gi        19Gi        21Gi       197Mi       147Gi       166Gi
	Swap:            0B          0B          0B

Graphics:
	0000:73:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104GL [Quadro P4000] [10de:1bb1] (rev a1)	
	Subsystem: Dell GP104GL [Quadro P4000] [1028:11a3]	
	Kernel driver in use: nvidia
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: UnassignedStructure Editing
Owner: set to Eric Pettersen
Platform: all
Project: ChimeraX
Status: newaccepted
Summary: ChimeraX bug report submissionError when building single nucleotide

comment:2 by Eric Pettersen, 4 years ago

Resolution: fixed
Status: acceptedclosed
Note: See TracTickets for help on using tickets.