Opened 5 years ago

Closed 5 years ago

Last modified 5 years ago

#4010 closed defect (fixed)

Adding second residue to Chain makes new Chain

Reported by: daniel.palma.i@… 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-5.8.18-1-MANJARO-x86_64-with-arch-Manjaro-Linux
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
Not quite sure if this is a bug or I am misunderstanding something. In the example script that i have send, when I add one atom to the structure (num_atoms == 1) and create a "missing structure" pseudobond between the atom and the backbone , the original Chain is extended, but if add more atoms (num_atoms >= 1) that connect to this new atom, a new Chain is created, instead of extending the original Chain.

Log:
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 2efv

2efv title:  
Crystal Structure of a Hypothetical Protein(MJ0366) from Methanocaldococcus
jannaschii [more info...]  
  
Chain information for 2efv #1  
---  
Chain | Description  
A | Hypothetical protein MJ0366  
  
Non-standard residues in 2efv #1  
---  
PO4 — phosphate ion  
  
2efv mmCIF Assemblies  
---  
1| author_defined_assembly  
  
num_atoms: 1  
Before adding atoms:  
/A  
/A LEU 83  
/A VAL 84  
/A LYS 85  
/A LEU 86  
/A ASP 87  
  
After adding atoms:  
/A  
/A VAL 84  
/A LYS 85  
/A LEU 86  
/A ASP 87  
/A UNK 88  
  

> open 2efv

2efv title:  
Crystal Structure of a Hypothetical Protein(MJ0366) from Methanocaldococcus
jannaschii [more info...]  
  
Chain information for 2efv #2  
---  
Chain | Description  
A | Hypothetical protein MJ0366  
  
Non-standard residues in 2efv #2  
---  
PO4 — phosphate ion  
  
2efv mmCIF Assemblies  
---  
1| author_defined_assembly  
  
num_atoms: 2  
Before adding atoms:  
2efv #2/A  
2efv #2/A LEU 83  
2efv #2/A VAL 84  
2efv #2/A LYS 85  
2efv #2/A LEU 86  
2efv #2/A ASP 87  
  
After adding atoms:  
2efv #2/A  
2efv #2/A VAL 84  
2efv #2/A LYS 85  
2efv #2/A LEU 86  
2efv #2/A ASP 87  
2efv #2/A UNK 88  
  
2efv #2/A  
2efv #2/A UNK 88  
2efv #2/A UNK 89  
  




OpenGL version: 4.6 (Core Profile) Mesa 20.2.3
OpenGL renderer: AMD Radeon(TM) Vega 8 Graphics (RAVEN, DRM 3.38.0, 5.8.18-1-MANJARO, LLVM 11.0.0)
OpenGL vendor: X.Org
Manufacturer: Acer
Model: Aspire A315-41
OS: Manjaro Linux 20.2 Nibia
Architecture: 64bit ELF
CPU: 8 AMD Ryzen 5 2500U with Radeon Vega Mobile Gfx
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           10Gi       4.6Gi       1.5Gi       197Mi       4.6Gi       5.6Gi
	Swap:          22Gi          0B        22Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: Advanced Micro Devices, Inc. [AMD/ATI] Raven Ridge [Radeon Vega Series / Radeon Vega Mobile Series] [1002:15dd] (rev c4)	
	Subsystem: Acer Incorporated [ALI] Device [1025:1259]	
	Kernel driver in use: amdgpu
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    appdirs: 1.4.4
    argparse: 1.4.0
    astroid: 2.4.2
    Babel: 2.8.0
    backcall: 0.2.0
    biopython: 1.78
    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-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
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    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-CythonTest: 0.3.1
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-Dummy: 0.2.0
    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-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-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
    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
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    jedi: 0.17.2
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    pip: 20.2.2
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    pydicom: 2.0.0
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    PyOpenGL: 3.1.5
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    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
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    Sphinx: 3.1.1
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File attachment: pseudobond_test.py

pseudobond_test.py​

Attachments (1)

pseudobond_test.py​ (1.3 KB ) - added by daniel.palma.i@… 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (4)

by daniel.palma.i@…, 5 years ago

Attachment: pseudobond_test.py​ added

Added by email2trac

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 → Adding second residue to Chain makes new Chain

The >1 case looks like a bug to me.

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

Apparently already fixed in the daily build. However, the daily build is returning (structure, status) from the "open" command rather than ([structure], status), and therefore the subscripting has to be just [0] instead of [0][0] for the script to run. I believe "open" should always return ([structure], status) (as it does in the 1.1 release) for ease of scripting (NMR ensembles can return a list of multiple structures) -- so I will fix that today.

comment:3 by Eric Pettersen, 5 years ago

Had that last comment all wrong. Didn't realize that the 1.1 release returned a list of lists rather than just a list of models. The daily build is doing the right thing in returning just a list of models.

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