Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#4151 closed defect (fixed)

struct_edit.add_bond trying to '+' Residues collections

Reported by: Tristan Croll 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-3.10.0-1127.19.1.el7.x86_64-x86_64-with-centos-7.8.2003-Core
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Suspect this may already be fixed in the daily builds, but reporting just in case.

Log:
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available

> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available

> alias st isolde step $*

> alias aw isolde add water $*

> alias awsf isolde add water sim false

UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open working.pdb

Summary of feedback from opening working.pdb  
---  
warnings | Ignored bad PDB record found on line 243  
LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN  
  
Ignored bad PDB record found on line 244  
LINKR TYR L 184 LEU L 186 gap  
  
Ignored bad PDB record found on line 245  
LINKR VAL L 210 GLU L 212 gap  
  
Ignored bad PDB record found on line 246  
LINKR PRO A 140 GLY A 148 gap  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in working.pdb #1  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  

> isolde start

> set selectionWidth 4

working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Non-standard residues in working.pdb #1.2  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  
Done loading forcefield  
Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> view /B:92

Loading residue template for GOL from internal database  
Loading residue template for SO4 from internal database  
Updating bulk solvent parameters...  

> select clear

> select clear

Updating bulk solvent parameters...  

> view /A:59

> select clear

Updating bulk solvent parameters...  

> view /A:213

> select clear

Updating bulk solvent parameters...  

> view /A:179

> view /H:179

> ui tool show Shell

/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved  
warn("IPython History requires SQLite, your history will not be saved")  

> select clear

> select clear

Updating bulk solvent parameters...  

> save working.pdb #1

> close #1

Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_18  
Deleting (LIVE) MDFF potential  

> open working_refine_001.pdb

Chain information for working_refine_001.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Chain information for working_refine_001.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> open
> /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb

Summary of feedback from opening
/run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb  
---  
warnings | Ignored bad PDB record found on line 243  
LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN  
  
Ignored bad PDB record found on line 244  
LINKR TYR L 184 LEU L 186 gap  
  
Ignored bad PDB record found on line 245  
LINKR VAL L 210 GLU L 212 gap  
  
Ignored bad PDB record found on line 246  
LINKR PRO A 140 GLY A 148 gap  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in working.pdb #2  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  

> close #2

> close #1

Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_18  
Deleting (LIVE) MDFF potential  

> open
> /run/media/tic20/storage/structure_dump/papers/2020_study_weekend/examples/3fyj_ref_3fhr/ref_to_isolde_rebuild/Refine_56/3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb
> format pdb

Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb #1  
---  
Chain | Description  
X | No description available  
  
Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb  
---  
Chain | Description  
1.2/X | No description available  
  

> close #1

> open working.pdb

Summary of feedback from opening working.pdb  
---  
warnings | Ignored bad PDB record found on line 243  
LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN  
  
Ignored bad PDB record found on line 244  
LINKR TYR L 184 LEU L 186 gap  
  
Ignored bad PDB record found on line 245  
LINKR VAL L 210 GLU L 212 gap  
  
Ignored bad PDB record found on line 246  
LINKR PRO A 140 GLY A 148 gap  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in working.pdb #1  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Non-standard residues in working.pdb #1.2  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  

> view /R:449

> delete /R:616

Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> set bgColor white

Loading residue template for POL from internal database  

> select clear

Updating bulk solvent parameters...  

> open 6m0j

6m0j title:  
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j #2  
---  
Chain | Description  
A | Angiotensin-converting enzyme 2  
E | Spike receptor binding domain  
  
Non-standard residues in 6m0j #2  
---  
CL — chloride ion  
NAG — N-acetyl-D-glucosamine  
ZN — zinc ion  
  

> matchmaker #2 to #1/R

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 working.pdb, chain R (#1.2) with 6m0j, chain E (#2), sequence
alignment score = 1012.9  
RMSD between 192 pruned atom pairs is 0.602 angstroms; (across all 194 pairs:
0.726)  
  

> show #2

> close #2

> view /R:604

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select :HOH

1284 atoms, 856 bonds, 428 residues, 1 model selected  

> clipper isolate sel contextDistance 0

> clipper isolate sel contextDistance 0

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

Updating bulk solvent parameters...  

> select :HOH

1281 atoms, 854 bonds, 427 residues, 1 model selected  

> delete sel

> close #1

Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)  
Deleting (LIVE) 2mFo-DFc  
Deleting (LIVE) mFo-DFc  
Deleting (LIVE) 2mFo-DFc_smooth_18  
Deleting (LIVE) MDFF potential  

> open working.pdb

Summary of feedback from opening working.pdb  
---  
warnings | Ignored bad PDB record found on line 243  
LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN  
  
Ignored bad PDB record found on line 244  
LINKR TYR L 184 LEU L 186 gap  
  
Ignored bad PDB record found on line 245  
LINKR VAL L 210 GLU L 212 gap  
  
Ignored bad PDB record found on line 246  
LINKR PRO A 140 GLY A 148 gap  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
  
Non-standard residues in working.pdb #1  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  
working.pdb title:  
\--- [more info...]  
  
Chain information for working.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/R | No description available  
  
Non-standard residues in working.pdb #1.2  
---  
CL — (CL)  
GOL — (GOL)  
NAG — (NAG)  
POL — (POL)  
SO4 — (SO4)  
  
Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM Y  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  

> select up

6 atoms, 4 bonds, 2 residues, 1 model selected  

> delete sel

> select clear

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

> select #1

17592 atoms, 17354 bonds, 2 pseudobonds, 1532 residues, 30 models selected  
Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

> select clear

Updating bulk solvent parameters...  

> view /R:449

> select up

21 atoms, 21 bonds, 1 residue, 1 model selected  

> select clear

> select clear

Updating bulk solvent parameters...  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> view /R:449

> awsf

> awsf

> awsf

> awsf

> awsf

> select clear

Updating bulk solvent parameters...  

> st first

> st

> st interp 2

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> aw

> isolde sim start sel

Updating bulk solvent parameters...  

> st

> st

> st

> st

> aw

> isolde sim start sel

> select clear

Updating bulk solvent parameters...  

> aw

> isolde sim start sel

Updating bulk solvent parameters...  

> st

> st

> st

> st

> st

> aw

> isolde sim start sel

> select clear

Updating bulk solvent parameters...  

> st

> aw

> isolde sim start sel

> select clear

Updating bulk solvent parameters...  

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> st

> aw

> isolde sim start sel

Updating bulk solvent parameters...  

> awsf

> awsf

> awsf

> select clear

Updating bulk solvent parameters...  

> select up

9 atoms, 6 bonds, 3 residues, 1 model selected  

> delete sel

> st

> st

> st

> st

> st

> st

> aw

> isolde sim start sel

> select clear

Updating bulk solvent parameters...  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> alias al isolde add ligand $*

> alias so setattr sel atoms occupancy $*

> al SO4

> so 0.7

Assigning occupancy attribute to 5 items  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  
Updating bulk solvent parameters...  

> select up

5 atoms, 4 bonds, 1 residue, 1 model selected  

> so 0.5

Assigning occupancy attribute to 5 items  

> st

> st

> st

> st

> st

> awsf

> awsf

Updating bulk solvent parameters...  

> st

> st

> st

> al GOL

> select clear

Updating bulk solvent parameters...  

> st

> aw

> isolde sim start sel

Updating bulk solvent parameters...  

> awsf

> awsf

Updating bulk solvent parameters...  

> select up

9 atoms, 6 bonds, 3 residues, 1 model selected  

> delete sel

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> delete sel

> al BMA

Deleted the following atoms from residue BMA R710: HO1, O1  

> show sel

> ui mousemode right "translate selected atoms"

> delete sel

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py", line
1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/menu/menu.py", line 58, in f  
module.run_script(session)  
File "/home/tic20/.local/share/ChimeraX/1.1/site-
packages/chimerax/isolde/menu/model_building/make_bond.py", line 22, in
run_script  
add_bond(*sel)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/struct_edit.py", line 225, in add_bond  
\+ all_residues[i1+1:i2] + all_residues[end_range+1:]  
TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'  
  
TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/atomic/struct_edit.py", line 225, in add_bond  
\+ all_residues[i1+1:i2] + all_residues[end_range+1:]  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            62G         12G         37G        261M         13G         49G
	Swap:          4.9G          0B        4.9G

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:11df]	
	Kernel driver in use: nvidia
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Async: 0.1
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-Phenix: 0.1
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    graphviz: 0.14.1
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    objgraph: 3.4.1
    openvr: 1.12.501
    packaging: 20.4
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    Send2Trash: 1.5.0
    SEQCROW: 0.20
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    versioneer: 0.18
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (6)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Structure Editing
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → struct_edit.add_bond trying to '+' Residues collections

in reply to:  2 ; comment:2 by Tristan Croll, 5 years ago 

Extra detail: I'd just added a new residue (BMA) - my code just appends this to the end of the model's residues - and went to link it back to an existing NAG.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 21 January 2021 16:42
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #4151: ChimeraX bug report submission

#4151: ChimeraX bug report submission
---------------------------+-----------------------------
 Reporter:  Tristan Croll  |                Type:  defect
   Status:  new            |            Priority:  normal
Component:  Unassigned     |          Blocked By:
 Blocking:                 |  Notify when closed:
---------------------------+-----------------------------
 {{{
 The following bug report has been submitted:
 Platform:        Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-
 centos-7.8.2003-Core
 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
 Description
 Suspect this may already be fixed in the daily builds, but reporting just
 in case.

 Log:
 > alias preview_toolshed toolshed url https://cxtoolshed-
 > preview.rbvi.ucsf.edu; toolshed reload available

 > alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
 > toolshed reload available

 > alias st isolde step $*

 > alias aw isolde add water $*

 > alias awsf isolde add water sim false

 UCSF ChimeraX version: 1.1 (2020-09-09)
 © 2016-2020 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open working.pdb

 Summary of feedback from opening working.pdb
 ---
 warnings | Ignored bad PDB record found on line 243
 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN

 Ignored bad PDB record found on line 244
 LINKR TYR L 184 LEU L 186 gap

 Ignored bad PDB record found on line 245
 LINKR VAL L 210 GLU L 212 gap

 Ignored bad PDB record found on line 246
 LINKR PRO A 140 GLY A 148 gap

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb #1
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Non-standard residues in working.pdb #1
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)


 > isolde start

 > set selectionWidth 4

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb
 ---
 Chain | Description
 1.2/A | No description available
 1.2/B | No description available
 1.2/H | No description available
 1.2/L | No description available
 1.2/R | No description available

 Non-standard residues in working.pdb #1.2
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)

 Done loading forcefield
 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
 Y
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 > view /B:92

 Loading residue template for GOL from internal database
 Loading residue template for SO4 from internal database
 Updating bulk solvent parameters...

 > select clear

 > select clear

 Updating bulk solvent parameters...

 > view /A:59

 > select clear

 Updating bulk solvent parameters...

 > view /A:213

 > select clear

 Updating bulk solvent parameters...

 > view /A:179

 > view /H:179

 > ui tool show Shell

 /opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/IPython/core/history.py:226:
 UserWarning: IPython History requires SQLite, your history will not be
 saved
 warn("IPython History requires SQLite, your history will not be saved")

 > select clear

 > select clear

 Updating bulk solvent parameters...

 > save working.pdb #1

 > close #1

 Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_smooth_18
 Deleting (LIVE) MDFF potential

 > open working_refine_001.pdb

 Chain information for working_refine_001.pdb #1
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Chain information for working_refine_001.pdb
 ---
 Chain | Description
 1.2/A | No description available
 1.2/B | No description available
 1.2/H | No description available
 1.2/L | No description available
 1.2/R | No description available

 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
 Y
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 > open
 >
 /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb

 Summary of feedback from opening
 /run/media/tic20/storage/structure_dump/consultancy/vir/2021_01_90qnB2/working.pdb
 ---
 warnings | Ignored bad PDB record found on line 243
 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN

 Ignored bad PDB record found on line 244
 LINKR TYR L 184 LEU L 186 gap

 Ignored bad PDB record found on line 245
 LINKR VAL L 210 GLU L 212 gap

 Ignored bad PDB record found on line 246
 LINKR PRO A 140 GLY A 148 gap

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb #2
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Non-standard residues in working.pdb #2
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)


 > close #2

 > close #1

 Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_smooth_18
 Deleting (LIVE) MDFF potential

 > open
 >
 /run/media/tic20/storage/structure_dump/papers/2020_study_weekend/examples/3fyj_ref_3fhr/ref_to_isolde_rebuild/Refine_56/3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb
 > format pdb

 Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb #1
 ---
 Chain | Description
 X | No description available

 Chain information for 3fyj_ref_to_3fhr_isolde_rebuild_refine_56.pdb
 ---
 Chain | Description
 1.2/X | No description available


 > close #1

 > open working.pdb

 Summary of feedback from opening working.pdb
 ---
 warnings | Ignored bad PDB record found on line 243
 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN

 Ignored bad PDB record found on line 244
 LINKR TYR L 184 LEU L 186 gap

 Ignored bad PDB record found on line 245
 LINKR VAL L 210 GLU L 212 gap

 Ignored bad PDB record found on line 246
 LINKR PRO A 140 GLY A 148 gap

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb #1
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Non-standard residues in working.pdb #1
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb
 ---
 Chain | Description
 1.2/A | No description available
 1.2/B | No description available
 1.2/H | No description available
 1.2/L | No description available
 1.2/R | No description available

 Non-standard residues in working.pdb #1.2
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)


 > view /R:449

 > delete /R:616

 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
 Y
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 > set bgColor white

 Loading residue template for POL from internal database

 > select clear

 Updating bulk solvent parameters...

 > open 6m0j

 6m0j title:
 Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with
 ACE2
 [more info...]

 Chain information for 6m0j #2
 ---
 Chain | Description
 A | Angiotensin-converting enzyme 2
 E | Spike receptor binding domain

 Non-standard residues in 6m0j #2
 ---
 CL — chloride ion
 NAG — N-acetyl-D-glucosamine
 ZN — zinc ion


 > matchmaker #2 to #1/R

 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 working.pdb, chain R (#1.2) with 6m0j, chain E (#2), sequence
 alignment score = 1012.9
 RMSD between 192 pruned atom pairs is 0.602 angstroms; (across all 194
 pairs:
 0.726)


 > show #2

 > close #2

 > view /R:604

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > select :HOH

 1284 atoms, 856 bonds, 428 residues, 1 model selected

 > clipper isolate sel contextDistance 0

 > clipper isolate sel contextDistance 0

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > select clear

 Updating bulk solvent parameters...

 > select :HOH

 1281 atoms, 854 bonds, 427 residues, 1 model selected

 > delete sel

 > close #1

 Deleting Crystallographic maps (90qnB2_2-1_uniqueifyCC.mtz)
 Deleting (LIVE) 2mFo-DFc
 Deleting (LIVE) mFo-DFc
 Deleting (LIVE) 2mFo-DFc_smooth_18
 Deleting (LIVE) MDFF potential

 > open working.pdb

 Summary of feedback from opening working.pdb
 ---
 warnings | Ignored bad PDB record found on line 243
 LINKR C1 NAG R 601 ND2 ASN R 343 NAG-ASN

 Ignored bad PDB record found on line 244
 LINKR TYR L 184 LEU L 186 gap

 Ignored bad PDB record found on line 245
 LINKR VAL L 210 GLU L 212 gap

 Ignored bad PDB record found on line 246
 LINKR PRO A 140 GLY A 148 gap

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb #1
 ---
 Chain | Description
 A | No description available
 B | No description available
 H | No description available
 L | No description available
 R | No description available

 Non-standard residues in working.pdb #1
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)

 working.pdb title:
 \--- [more info...]

 Chain information for working.pdb
 ---
 Chain | Description
 1.2/A | No description available
 1.2/B | No description available
 1.2/H | No description available
 1.2/L | No description available
 1.2/R | No description available

 Non-standard residues in working.pdb #1.2
 ---
 CL — (CL)
 GOL — (GOL)
 NAG — (NAG)
 POL — (POL)
 SO4 — (SO4)

 Discarding unrecognised/unsupported data array /XDScrystal/XDSdataset/ISYM
 Y
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 > select up

 6 atoms, 4 bonds, 2 residues, 1 model selected

 > delete sel

 > select clear

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > select clear

 > select #1

 17592 atoms, 17354 bonds, 2 pseudobonds, 1532 residues, 30 models selected
 Map is too large for fast cubic interpolation on the GPU! Switching to
 slower,
 more memory-efficient implementation.

 > select clear

 Updating bulk solvent parameters...

 > view /R:449

 > select up

 21 atoms, 21 bonds, 1 residue, 1 model selected

 > select clear

 > select clear

 Updating bulk solvent parameters...

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > view /R:449

 > awsf

 > awsf

 > awsf

 > awsf

 > awsf

 > select clear

 Updating bulk solvent parameters...

 > st first

 > st

 > st interp 2

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 Updating bulk solvent parameters...

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 > select clear

 Updating bulk solvent parameters...

 > aw

 > isolde sim start sel

 Updating bulk solvent parameters...

 > st

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 > select clear

 Updating bulk solvent parameters...

 > st

 > aw

 > isolde sim start sel

 > select clear

 Updating bulk solvent parameters...

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 Updating bulk solvent parameters...

 > awsf

 > awsf

 > awsf

 > select clear

 Updating bulk solvent parameters...

 > select up

 9 atoms, 6 bonds, 3 residues, 1 model selected

 > delete sel

 > st

 > st

 > st

 > st

 > st

 > st

 > aw

 > isolde sim start sel

 > select clear

 Updating bulk solvent parameters...

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > alias al isolde add ligand $*

 > alias so setattr sel atoms occupancy $*

 > al SO4

 > so 0.7

 Assigning occupancy attribute to 5 items

 > select up

 5 atoms, 4 bonds, 1 residue, 1 model selected
 Updating bulk solvent parameters...

 > select up

 5 atoms, 4 bonds, 1 residue, 1 model selected

 > so 0.5

 Assigning occupancy attribute to 5 items

 > st

 > st

 > st

 > st

 > st

 > awsf

 > awsf

 Updating bulk solvent parameters...

 > st

 > st

 > st

 > al GOL

 > select clear

 Updating bulk solvent parameters...

 > st

 > aw

 > isolde sim start sel

 Updating bulk solvent parameters...

 > awsf

 > awsf

 Updating bulk solvent parameters...

 > select up

 9 atoms, 6 bonds, 3 residues, 1 model selected

 > delete sel

 > select up

 3 atoms, 2 bonds, 1 residue, 1 model selected

 > delete sel

 > al BMA

 Deleted the following atoms from residue BMA R710: HO1, O1

 > show sel

 > ui mousemode right "translate selected atoms"

 > delete sel

 Traceback (most recent call last):
 File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/ui/gui.py",
 line
 1574, in <lambda>
 action.triggered.connect(lambda arg, cb = callback: cb())
 File "/home/tic20/.local/share/ChimeraX/1.1/site-
 packages/chimerax/isolde/menu/menu.py", line 58, in f
 module.run_script(session)
 File "/home/tic20/.local/share/ChimeraX/1.1/site-
 packages/chimerax/isolde/menu/model_building/make_bond.py", line 22, in
 run_script
 add_bond(*sel)
 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/atomic/struct_edit.py", line 225, in add_bond
 \+ all_residues[i1+1:i2] + all_residues[end_range+1:]
 TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'

 TypeError: unsupported operand type(s) for +: 'Residues' and 'Residues'

 File "/opt/UCSF/ChimeraX/lib/python3.7/site-
 packages/chimerax/atomic/struct_edit.py", line 225, in add_bond
 \+ all_residues[i1+1:i2] + all_residues[end_range+1:]

 See log for complete Python traceback.





 OpenGL version: 3.3.0 NVIDIA 455.32.00
 OpenGL renderer: TITAN Xp/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Dell Inc.
 Model: Precision T5600
 OS: CentOS Linux 7 Core
 Architecture: 64bit ELF
 CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
 Cache Size: 20480 KB
 Memory:
                       total        used        free      shared
 buff/cache   available
         Mem:            62G         12G         37G        261M
 13G         49G
         Swap:          4.9G          0B        4.9G

 Graphics:
         03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102
 [TITAN Xp] [10de:1b02] (rev a1)
         Subsystem: NVIDIA Corporation Device [10de:11df]
         Kernel driver in use: nvidia
 PyQt version: 5.12.3
 Compiled Qt version: 5.12.4
 Runtime Qt version: 5.12.9
 Installed Packages:
     alabaster: 0.7.12
     appdirs: 1.4.4
     Babel: 2.8.0
     backcall: 0.2.0
     blockdiag: 2.0.1
     certifi: 2020.6.20
     chardet: 3.0.4
     ChimeraX-AddH: 2.1.1
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.1
     ChimeraX-Arrays: 1.0
     ChimeraX-Async: 0.1
     ChimeraX-Atomic: 1.6.1
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 1.0.1
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.0
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.0
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.1
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.0
     ChimeraX-Clipper: 0.15.0
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-CommandLine: 1.1.3
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.1
     ChimeraX-CoreFormats: 1.0
     ChimeraX-coulombic: 1.0.1
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-DataFormats: 1.0
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1
     ChimeraX-DistUI: 1.0
     ChimeraX-Dssp: 2.0
     ChimeraX-EMDB-SFF: 1.0
     ChimeraX-ExperimentalCommands: 1.0
     ChimeraX-FileHistory: 1.0
     ChimeraX-FunctionKey: 1.0
     ChimeraX-Geometry: 1.1
     ChimeraX-gltf: 1.0
     ChimeraX-Graphics: 1.0
     ChimeraX-Hbonds: 2.0
     ChimeraX-Help: 1.0
     ChimeraX-HKCage: 1.3
     ChimeraX-IHM: 1.0
     ChimeraX-ImageFormats: 1.0
     ChimeraX-IMOD: 1.0
     ChimeraX-IO: 1.0
     ChimeraX-ISOLDE: 1.1.0
     ChimeraX-Label: 1.0
     ChimeraX-LinuxSupport: 1.0
     ChimeraX-ListInfo: 1.0
     ChimeraX-Log: 1.1.1
     ChimeraX-LookingGlass: 1.1
     ChimeraX-Map: 1.0.1
     ChimeraX-MapData: 2.0
     ChimeraX-MapEraser: 1.0
     ChimeraX-MapFilter: 2.0
     ChimeraX-MapFit: 2.0
     ChimeraX-MapSeries: 2.0
     ChimeraX-Markers: 1.0
     ChimeraX-Mask: 1.0
     ChimeraX-MatchMaker: 1.1
     ChimeraX-MDcrds: 2.0
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.0
     ChimeraX-mmCIF: 2.2
     ChimeraX-MMTF: 2.0
     ChimeraX-Modeller: 1.0
     ChimeraX-ModelPanel: 1.0
     ChimeraX-ModelSeries: 1.0
     ChimeraX-Mol2: 2.0
     ChimeraX-Morph: 1.0
     ChimeraX-MouseModes: 1.0
     ChimeraX-Movie: 1.0
     ChimeraX-Neuron: 1.0
     ChimeraX-Nucleotides: 2.0
     ChimeraX-OpenCommand: 1.2.1
     ChimeraX-PDB: 2.1
     ChimeraX-PDBBio: 1.0
     ChimeraX-Phenix: 0.1
     ChimeraX-PickBlobs: 1.0
     ChimeraX-Positions: 1.0
     ChimeraX-PresetMgr: 1.0
     ChimeraX-PubChem: 2.0
     ChimeraX-Read-Pbonds: 1.0
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.0
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-SaveCommand: 1.2
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SeqView: 2.2
     ChimeraX-Shape: 1.0.1
     ChimeraX-Shell: 1.0
     ChimeraX-Shortcuts: 1.0
     ChimeraX-ShowAttr: 1.0
     ChimeraX-ShowSequences: 1.0
     ChimeraX-SideView: 1.0
     ChimeraX-Smiles: 2.0
     ChimeraX-SmoothLines: 1.0
     ChimeraX-SpaceNavigator: 1.0
     ChimeraX-StdCommands: 1.0.4
     ChimeraX-STL: 1.0
     ChimeraX-Storm: 1.0
     ChimeraX-Struts: 1.0
     ChimeraX-Surface: 1.0
     ChimeraX-SwapAA: 2.0
     ChimeraX-SwapRes: 2.0
     ChimeraX-TapeMeasure: 1.0
     ChimeraX-Test: 1.0
     ChimeraX-Toolbar: 1.0
     ChimeraX-ToolshedUtils: 1.0
     ChimeraX-Tug: 1.0
     ChimeraX-UI: 1.2.3
     ChimeraX-uniprot: 2.0
     ChimeraX-ViewDockX: 1.0
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.3
     comtypes: 1.1.7
     cxservices: 1.0
     cycler: 0.10.0
     Cython: 0.29.20
     decorator: 4.4.2
     distlib: 0.3.1
     distro: 1.5.0
     docutils: 0.16
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     graphviz: 0.14.1
     h5py: 2.10.0
     html2text: 2020.1.16
     idna: 2.10
     ihm: 0.16
     imagecodecs: 2020.5.30
     imagecodecs-lite: 2020.1.31
     imagesize: 1.2.0
     ipykernel: 5.3.0
     ipython: 7.15.0
     ipython-genutils: 0.2.0
     jedi: 0.17.2
     Jinja2: 2.11.2
     jupyter-client: 6.1.3
     jupyter-core: 4.6.3
     kiwisolver: 1.2.0
     line-profiler: 2.1.2
     lxml: 4.5.1
     MarkupSafe: 1.1.1
     matplotlib: 3.2.1
     msgpack: 1.0.0
     netifaces: 0.10.9
     networkx: 2.4
     numexpr: 2.7.1
     numpy: 1.18.5
     numpydoc: 1.0.0
     objgraph: 3.4.1
     openvr: 1.12.501
     packaging: 20.4
     ParmEd: 3.2.0
     parso: 0.7.1
     pexpect: 4.8.0
     pickleshare: 0.7.5
     Pillow: 7.1.2
     pip: 20.2.2
     pkginfo: 1.5.0.1
     prompt-toolkit: 3.0.7
     psutil: 5.7.0
     ptyprocess: 0.6.0
     pycollada: 0.7.1
     pydicom: 2.0.0
     Pygments: 2.6.1
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 2.4.7
     PyQt5-commercial: 5.12.3
     PyQt5-sip: 4.19.19
     PyQtWebEngine-commercial: 5.12.1
     python-dateutil: 2.8.1
     pytz: 2020.1
     pyzmq: 19.0.2
     qtconsole: 4.7.4
     QtPy: 1.9.0
     RandomWords: 0.3.0
     requests: 2.24.0
     scipy: 1.4.1
     Send2Trash: 1.5.0
     SEQCROW: 0.20
     setuptools: 49.4.0
     sfftk-rw: 0.6.6.dev0
     six: 1.15.0
     snowballstemmer: 2.0.0
     sortedcontainers: 2.2.2
     Sphinx: 3.1.1
     sphinxcontrib-applehelp: 1.0.2
     sphinxcontrib-blockdiag: 2.0.0
     sphinxcontrib-devhelp: 1.0.2
     sphinxcontrib-htmlhelp: 1.0.3
     sphinxcontrib-jsmath: 1.0.1
     sphinxcontrib-qthelp: 1.0.3
     sphinxcontrib-serializinghtml: 1.1.4
     suds-jurko: 0.6
     tables: 3.6.1
     tifffile: 2020.6.3
     tinyarray: 1.2.2
     tornado: 6.0.4
     traitlets: 5.0.4
     urllib3: 1.25.10
     versioneer: 0.18
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.34.2

 }}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4151>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:3 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

You are right that it is fixed in the daily build, but I don't understand why it isn't fixed in the 1.1 release. The fix was made Sep. 2 and the release was Sep. 9. I must have forgotten to put the fix on the master branch? I guess that's what happened.

--Eric

in reply to:  4 ; comment:4 by Tristan Croll, 5 years ago 

Sounds like it's time for me to catch up to the daily builds again! Any projected date for ChimeraX 1.2?
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 21 January 2021 17:57
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4151: struct_edit.add_bond trying to '+' Residues collections

#4151: struct_edit.add_bond trying to '+' Residues collections
----------------------------------------+----------------------------
          Reporter:  Tristan Croll      |      Owner:  Eric Pettersen
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:  fixed              |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => fixed


Comment:

 You are right that it is fixed in the daily build, but I don't understand
 why it isn't fixed in the 1.1 release.  The fix was made Sep. 2 and the
 release was Sep. 9.  I must have forgotten to put the fix on the master
 branch?  I guess that's what happened.

 --Eric

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4151#comment:3>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:5 by Eric Pettersen, 5 years ago

Chatter has been for sometime in February, to kind of match up with the end of our NETE contract.

--Eric

in reply to:  6 ; comment:6 by Tristan Croll, 5 years ago 

Thanks!
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 21 January 2021 18:13
Cc: pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #4151: struct_edit.add_bond trying to '+' Residues collections

#4151: struct_edit.add_bond trying to '+' Residues collections
----------------------------------------+----------------------------
          Reporter:  Tristan Croll      |      Owner:  Eric Pettersen
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:  fixed              |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------------

Comment (by Eric Pettersen):

 Chatter has been for sometime in February, to kind of match up with the
 end of our NETE contract.

 --Eric

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Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4151#comment:5>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
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