Opened 17 months ago

Closed 17 months ago

#15460 closed defect (duplicate)

Deleted bond reappears in saved mmCIF file

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

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.19045
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Deleted a bond in metal complex /A:344 and saved as mmCIF and opened saved file and bond came back.  Why?

Log:
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 7rf1

Summary of feedback from opening 7rf1 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /L:1  
Atom H1 is not in the residue template for MET /Z:1  
Atom H1 is not in the residue template for MET /z:1  
notes | Fetching compressed mmCIF 7rf1 from
http://files.rcsb.org/download/7rf1.cif  
Fetching CCD FE2 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/FE2/FE2.cif  
  
7rf1 title:  
RT XFEL structure of Photosystem II averaged across all S-states at 1.89
Angstrom resolution [more info...]  
  
Chain information for 7rf1 #1  
---  
Chain | Description | UniProt  
A a | Photosystem II protein D1 1 | PSBA1_THEEB 1-344  
B b | Photosystem II CP47 reaction center protein | PSBB_THEEB 1-510  
C c | Photosystem II CP43 reaction center protein | PSBC_THEEB 13-473  
D d | Photosystem II D2 protein | PSBD_THEEB 1-352  
E e | Cytochrome b559 subunit alpha | PSBE_THEEB 1-84  
F f | Cytochrome b559 subunit beta | PSBF_THEEB 1-45  
H h | Photosystem II reaction center protein H | PSBH_THEEB 1-66  
I i | Photosystem II reaction center protein I | PSBI_THEEB 1-38  
J j | Photosystem II reaction center protein J | PSBJ_THEEB 1-40  
K k | Photosystem II reaction center protein K | PSBK_THEEB 1-46  
L l | Photosystem II reaction center protein L | PSBL_THEEB 1-37  
M m | Photosystem II reaction center protein M | PSBM_THEEB 2-36  
O o | Photosystem II manganese-stabilizing polypeptide | PSBO_THEEB -25-246  
R r | Photosystem II protein Y | PSBY_THEEB 1-41  
T t | Photosystem II reaction center protein T | PSBT_THEEB 2-32  
U u | Photosystem II 12 kDa extrinsic protein | PSBU_THEEB -29-104  
V v | Cytochrome c-550 | CY550_THEEB -25-137  
X x | Photosystem II reaction center X protein | PSBX_THEEB 1-41  
Y y | Photosystem II reaction center protein Ycf12 | YCF12_THEEB 1-46  
Z z | Photosystem II reaction center protein Z | PSBZ_THEEB 1-62  
  
Non-standard residues in 7rf1 #1  
---  
BCR — β-carotene  
BCT — bicarbonate ion  
CL — chloride ion  
CLA — chlorophyll A  
DGD — digalactosyl diacyl glycerol (DGDG)  
FE2 — Fe (II) ion  
FME — N-formylmethionine  
HEC — heme C  
HEM — protoporphyrin IX containing Fe (HEME)  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMG — 1,2-distearoyl-monogalactosyl-diglyceride  
OEX — Ca-MN4-O5 cluster  
PHO — pheophytin A  
PL9 —
2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone
(plastoquinone 9)  
SQD — 1,2-di-O-acyl-3-O-[6-deoxy-6-sulfo-α-D-glucopyranosyl]-Sn-glycerol
(sulfoquinovosyldiacylglycerol)  
STE — stearic acid  
  

> hide ~/A

> select /A:344

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:344@CA

1 atom, 1 residue, 1 model selected  

> select sel :< 5

137 atoms, 134 bonds, 5 pseudobonds, 13 residues, 2 models selected  

> hide ~sel

> show /A:344 :<10

> select /A:182@N

1 atom, 1 residue, 1 model selected  

> select /A:185@N

1 atom, 1 residue, 1 model selected  

> select up

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select up

250 atoms, 253 bonds, 16 residues, 1 model selected  

> select down

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select down

1 atom, 1 residue, 1 model selected  

> select clear

> style stick

Changed 104128 atom styles  

> delete atoms sel

> delete bonds sel

> save test.cif

Fetching CCD STE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/STE/STE.cif  

> open C:\Users\goddard\Desktop\test.cif format mmcif

Chain information for test.cif #2  
---  
Chain | Description  
A a | Photosystem II protein D1 1  
B b | Photosystem II CP47 reaction center protein  
C c | Photosystem II CP43 reaction center protein  
D d | Photosystem II D2 protein  
E e | Cytochrome b559 subunit alpha  
F f | Cytochrome b559 subunit beta  
H h | Photosystem II reaction center protein H  
I i | Photosystem II reaction center protein I  
J j | Photosystem II reaction center protein J  
K k | Photosystem II reaction center protein K  
L l | Photosystem II reaction center protein L  
M m | Photosystem II reaction center protein M  
O o | Photosystem II manganese-stabilizing polypeptide  
R r | Photosystem II protein Y  
T t | Photosystem II reaction center protein T  
U u | Photosystem II 12 kDa extrinsic protein  
V v | Cytochrome c-550  
X x | Photosystem II reaction center X protein  
Y y | Photosystem II reaction center protein Ycf12  
Z z | Photosystem II reaction center protein Z  
  

> hide #!1 models

> view

> hide #2/A:344 :>10

> style #!2 stick

Changed 104128 atom styles  

> ~bond sel

> select #2/A:418@O5

1 atom, 1 residue, 1 model selected  

> select add #2/A:418@MN1

2 atoms, 1 residue, 1 model selected  

> bond sel

Created 0 bonds  

> help bond

> bond sel reasonable false

Created 1 bond  




OpenGL version: 3.3.0 NVIDIA 536.23
OpenGL renderer: NVIDIA GeForce RTX 4070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Gigabyte Technology Co., Ltd.
Model: To be filled by O.E.M.
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 66,135,482,368
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-RealSense: 1.9
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
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Change History (2)

comment:1 by Tom Goddard, 17 months ago

Cc: Tom Goddard added
Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Reporter: changed from goddard@… to abhowmick@…
Status: new → assigned
Summary: ChimeraX bug report submission → Deleted bond reappears in saved mmCIF file

I'll re-report this bug with a simpler Log.

comment:2 by Tom Goddard, 17 months ago

Resolution: → duplicate
Status: assigned → closed

Duplicate of #15461

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