Opened 4 years ago

Closed 4 years ago

#4881 closed defect (fixed)

Pseudobonds don't go to atom with ribbon when not hiding backbone atoms

Reported by: Tristan Croll Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc: Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.3.dev202106210544 (2021-06-21 05:44:33 UTC)
Description
When Residue.ribbon_hide_backbone is False, metal coordination bonds still go to the ribbon spline point rather than to the backbone oxygen. Replication:

open 5y5s
style stick
color byhet
cartoon suppress f
view /8:CA pad 0.7

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

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color bychain; color byhet
    cs	clipper set contourSensitivity {arguments}
    

  
UCSF ChimeraX version: 1.3.dev202106210544 (2021-06-21)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5y5s structureFactors true

Summary of feedback from opening 5y5s fetched from pdb  
---  
notes | Resolution: 1.9000011866375335  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 44,44,40, pixel
0.605,0.599,0.626, shown at level 0.34, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 44,44,40, pixel
0.605,0.599,0.626, shown at level -0.105,0.105, step 1, values float32  
Opened (LIVE) 2mFo-DFc_smooth_17 as #1.1.1.4, grid size 44,44,40, pixel
0.605,0.599,0.626, shown at level 0.286, step 1, values float32  
Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 44,44,40, pixel
0.605,0.599,0.626, shown at level -0.69,0.69, step 1, values float32  
5y5s title:  
Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom resolution
[more info...]  
  
Chain information for 5y5s  
---  
Chain | Description  
1.2/0 1.2/2 1.2/4 1.2/6 1.2/8 1.2/B 1.2/E 1.2/G 1.2/J 1.2/N 1.2/P 1.2/R 1.2/T
1.2/V 1.2/X 1.2/Z | LH1 β polypeptide  
1.2/1 1.2/3 1.2/5 1.2/7 1.2/9 1.2/A 1.2/D 1.2/F 1.2/I 1.2/K 1.2/O 1.2/Q 1.2/S
1.2/U 1.2/W 1.2/Y | LH1 α polypeptide  
1.2/C | Photosynthetic reaction center cytochrome c subunit  
1.2/H | Photosynthetic reaction center H subunit  
1.2/L | Photosynthetic reaction center L subunit  
1.2/M | Photosynthetic reaction center M subunit  
  
Non-standard residues in 5y5s #1.2  
---  
BCL — bacteriochlorophyll A  
BPH — bacteriopheophytin A  
CA — calcium ion  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
CRT — spirilloxanthin (rhodoviolascin)  
FE — Fe (III) ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
HEM — protoporphyrin IX containing Fe (HEME)  
LDA — lauryl dimethylamine-N-oxide  
LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole  
LMT — dodecyl-β-D-maltoside  
MG — magnesium ion  
MQ8 — menaquinone 8 (2-methyl-3-(3,7,11,15,19,23,27,31-octamethyl-
dotriaconta-2,6,10,14,18,22,26,30-octaenyl)-[1,4]napthoquinone)  
PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
(3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)  
PGV —
(1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl
(11E)-octadec-11-enoate (phosphatidylglycerol, 2-vaccenoyl-1-palmitoyl-Sn-
glycerol-3-phosphoglycerol)  
SO4 — sulfate ion  
UNL — unknown ligand  
UQ8 — Ubiquinone-8
(2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]cyclohexa-2,5-diene-1,4-dione)  
  

> view

> select :MG

1 atom, 1 residue, 1 model selected  

> select :CA

16 atoms, 16 residues, 1 model selected  

> clipper isolate sel

> clipper spotlight

> ui tool show Shell




OpenGL version: 3.3.0 NVIDIA 465.19.01
OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
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        9.1G         42G        274M         11G         52G
	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
Locale: ('en_GB', '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: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.7
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.23
    ChimeraX-AtomicLibrary: 3.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202106210544
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    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
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.3.dev20
    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: 1.2.1
    ChimeraX-MDcrds: 2.3
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
    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: 1.6
    ChimeraX-PDB: 2.4.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    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
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-Sample: 0.1
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.1
    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
    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: 1.10
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-Voyager: 0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.2.1
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 2.11.3
    jupyter-client: 6.1.12
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.5.1
    numexpr: 2.7.3
    numpy: 1.20.3
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.8.2
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.19
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.1.0
    qtconsole: 5.1.0
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.25.1
    scipy: 1.6.3
    setuptools: 57.0.0
    sfftk-rw: 0.7.0.post1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.4.0
    Sphinx: 4.0.1
    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: 5.0.5
    urllib3: 1.26.5
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0

Change History (3)

in reply to:  1 ; comment:1 by Tristan Croll, 4 years ago 

Same goes for distance pseudobonds.
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 09 July 2021 10:04
To: Tristan Croll <tic20@cam.ac.uk>
Subject: [ChimeraX] #4881: ChimeraX bug report submission

#4881: 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-3.10.0-1160.25.1.el7.x86_64-x86_64-with-glibc2.14
 ChimeraX Version: 1.3.dev202106210544 (2021-06-21 05:44:33 UTC)
 Description
 When Residue.ribbon_hide_backbone is False, metal coordination bonds still
 go to the ribbon spline point rather than to the backbone oxygen.
 Replication:

 open 5y5s
 style stick
 color byhet
 cartoon suppress f
 view /8:CA pad 0.7

 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

 > isolde shorthand


     Initialising ISOLDE-specific command aliases:
     Alias       Equivalent full command
     -------------------------------------------------
     st  isolde step {arguments}
     aw  isolde add water {arguments}
     awsf        isolde add water {arguments} sim false
     al  isolde add ligand {arguments}
     aa  isolde add aa $1 sel {arguments}
     ht  isolde mod his sel {arguments}
     so  setattr sel atoms occupancy {arguments}
     ab  isolde adjust bfactors {arguments}
     ss  isolde sim start sel
     rt  isolde release torsions sel {arguments}
     rd  isolde release distances sel {arguments}
     pf  isolde pepflip sel
     cf  isolde cisflip sel
     cbb color bfactor {arguments}
     cbo color byattr occupancy {arguments}
     cbc color bychain; color byhet
     cs  clipper set contourSensitivity {arguments}



 UCSF ChimeraX version: 1.3.dev202106210544 (2021-06-21)
 © 2016-2021 Regents of the University of California. All rights reserved.
 How to cite UCSF ChimeraX

 > open 5y5s structureFactors true

 Summary of feedback from opening 5y5s fetched from pdb
 ---
 notes | Resolution: 1.9000011866375335
 Reflection data provided as intensities. Performing French & Wilson
 scaling to
 convert to amplitudes...

 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 44,44,40, pixel
 0.605,0.599,0.626, shown at level 0.34, step 1, values float32
 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 44,44,40, pixel
 0.605,0.599,0.626, shown at level -0.105,0.105, step 1, values float32
 Opened (LIVE) 2mFo-DFc_smooth_17 as #1.1.1.4, grid size 44,44,40, pixel
 0.605,0.599,0.626, shown at level 0.286, step 1, values float32
 Opened (STATIC) F_calc, phase_calc as #1.1.1.5, grid size 44,44,40, pixel
 0.605,0.599,0.626, shown at level -0.69,0.69, step 1, values float32
 5y5s title:
 Structure of photosynthetic LH1-RC super-complex at 1.9 angstrom
 resolution
 [more info...]

 Chain information for 5y5s
 ---
 Chain | Description
 1.2/0 1.2/2 1.2/4 1.2/6 1.2/8 1.2/B 1.2/E 1.2/G 1.2/J 1.2/N 1.2/P 1.2/R
 1.2/T
 1.2/V 1.2/X 1.2/Z | LH1 β polypeptide
 1.2/1 1.2/3 1.2/5 1.2/7 1.2/9 1.2/A 1.2/D 1.2/F 1.2/I 1.2/K 1.2/O 1.2/Q
 1.2/S
 1.2/U 1.2/W 1.2/Y | LH1 α polypeptide
 1.2/C | Photosynthetic reaction center cytochrome c subunit
 1.2/H | Photosynthetic reaction center H subunit
 1.2/L | Photosynthetic reaction center L subunit
 1.2/M | Photosynthetic reaction center M subunit

 Non-standard residues in 5y5s #1.2
 ---
 BCL — bacteriochlorophyll A
 BPH — bacteriopheophytin A
 CA — calcium ion
 CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
 glycero-3-phospho)-1',3'-Sn-glycerol)
 CRT — spirilloxanthin (rhodoviolascin)
 FE — Fe (III) ion
 GOL — glycerol (glycerin; propane-1,2,3-triol)
 HEM — protoporphyrin IX containing Fe (HEME)
 LDA — lauryl dimethylamine-N-oxide
 LHG — 1,2-dipalmitoyl-phosphatidyl-glycerole
 LMT — dodecyl-β-D-maltoside
 MG — magnesium ion
 MQ8 — menaquinone 8 (2-methyl-3-(3,7,11,15,19,23,27,31-octamethyl-
 dotriaconta-2,6,10,14,18,22,26,30-octaenyl)-[1,4]napthoquinone)
 PEF — di-palmitoyl-3-Sn-phosphatidylethanolamine
 (3-[aminoethylphosphoryl]-[1,2-di-palmitoyl]-Sn-glycerol)
 PGV —
 (1R)-2-{[{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(palmitoyloxy)methyl]ethyl
 (11E)-octadec-11-enoate (phosphatidylglycerol, 2-vaccenoyl-1-palmitoyl-Sn-
 glycerol-3-phosphoglycerol)
 SO4 — sulfate ion
 UNL — unknown ligand
 UQ8 — Ubiquinone-8
 (2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-octaen-1-yl]cyclohexa-2,5-diene-1,4-dione)


 > view

 > select :MG

 1 atom, 1 residue, 1 model selected

 > select :CA

 16 atoms, 16 residues, 1 model selected

 > clipper isolate sel

 > clipper spotlight

 > ui tool show Shell




 OpenGL version: 3.3.0 NVIDIA 465.19.01
 OpenGL renderer: NVIDIA TITAN Xp/PCIe/SSE2
 OpenGL vendor: NVIDIA Corporation
 Manufacturer: Dell Inc.
 Model: Precision T5600
 OS: CentOS Linux 7 Core
 Architecture: 64bit ELF
 Virutal Machine: none
 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        9.1G         42G        274M
 11G         52G
         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
 Locale: ('en_GB', '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: 2021.5.30
     cftime: 1.5.0
     chardet: 4.0.0
     ChimeraX-AddCharge: 1.1.4
     ChimeraX-AddH: 2.1.7
     ChimeraX-AlignmentAlgorithms: 2.0
     ChimeraX-AlignmentHdrs: 3.2
     ChimeraX-AlignmentMatrices: 2.0
     ChimeraX-Alignments: 2.1
     ChimeraX-AmberInfo: 1.0
     ChimeraX-Arrays: 1.0
     ChimeraX-Atomic: 1.23
     ChimeraX-AtomicLibrary: 3.3
     ChimeraX-AtomSearch: 2.0
     ChimeraX-AtomSearchLibrary: 1.0
     ChimeraX-AxesPlanes: 2.0
     ChimeraX-BasicActions: 1.1
     ChimeraX-BILD: 1.0
     ChimeraX-BlastProtein: 1.1.1
     ChimeraX-BondRot: 2.0
     ChimeraX-BugReporter: 1.0
     ChimeraX-BuildStructure: 2.5.2
     ChimeraX-Bumps: 1.0
     ChimeraX-BundleBuilder: 1.1
     ChimeraX-ButtonPanel: 1.0
     ChimeraX-CageBuilder: 1.0
     ChimeraX-CellPack: 1.0
     ChimeraX-Centroids: 1.1
     ChimeraX-ChemGroup: 2.0
     ChimeraX-Clashes: 2.1
     ChimeraX-Clipper: 0.17.0
     ChimeraX-ColorActions: 1.0
     ChimeraX-ColorGlobe: 1.0
     ChimeraX-ColorKey: 1.3.2
     ChimeraX-CommandLine: 1.1.4
     ChimeraX-ConnectStructure: 2.0
     ChimeraX-Contacts: 1.0
     ChimeraX-Core: 1.3.dev202106210544
     ChimeraX-CoreFormats: 1.0
     ChimeraX-coulombic: 1.3
     ChimeraX-Crosslinks: 1.0
     ChimeraX-Crystal: 1.0
     ChimeraX-CrystalContacts: 1.0
     ChimeraX-DataFormats: 1.2
     ChimeraX-Dicom: 1.0
     ChimeraX-DistMonitor: 1.1.4
     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
     ChimeraX-Help: 1.1
     ChimeraX-HKCage: 1.3
     ChimeraX-IHM: 1.1
     ChimeraX-ImageFormats: 1.1
     ChimeraX-IMOD: 1.0
     ChimeraX-IO: 1.0.1
     ChimeraX-ISOLDE: 1.3.dev20
     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: 1.2.1
     ChimeraX-MDcrds: 2.3
     ChimeraX-MedicalToolbar: 1.0.1
     ChimeraX-Meeting: 1.0
     ChimeraX-MLP: 1.1
     ChimeraX-mmCIF: 2.3
     ChimeraX-MMTF: 2.1
     ChimeraX-Modeller: 1.0.2
     ChimeraX-ModelPanel: 1.1
     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: 1.6
     ChimeraX-PDB: 2.4.2
     ChimeraX-PDBBio: 1.0
     ChimeraX-PDBLibrary: 1.0.1
     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
     ChimeraX-Registration: 1.1
     ChimeraX-RemoteControl: 1.0
     ChimeraX-ResidueFit: 1.0
     ChimeraX-RestServer: 1.1
     ChimeraX-RNALayout: 1.0
     ChimeraX-RotamerLibMgr: 2.0
     ChimeraX-RotamerLibsDunbrack: 2.0
     ChimeraX-RotamerLibsDynameomics: 2.0
     ChimeraX-RotamerLibsRichardson: 2.0
     ChimeraX-Sample: 0.1
     ChimeraX-SaveCommand: 1.4
     ChimeraX-SchemeMgr: 1.0
     ChimeraX-SDF: 2.0
     ChimeraX-Segger: 1.0
     ChimeraX-Segment: 1.0
     ChimeraX-SelInspector: 1.0
     ChimeraX-SeqView: 2.4.1
     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
     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: 1.10
     ChimeraX-uniprot: 2.1
     ChimeraX-UnitCell: 1.0
     ChimeraX-ViewDockX: 1.0.1
     ChimeraX-Vive: 1.1
     ChimeraX-VolumeMenu: 1.0
     ChimeraX-Voyager: 0.1
     ChimeraX-VTK: 1.0
     ChimeraX-WavefrontOBJ: 1.0
     ChimeraX-WebCam: 1.0
     ChimeraX-WebServices: 1.0
     ChimeraX-Zone: 1.0
     colorama: 0.4.4
     comtypes: 1.1.10
     cxservices: 1.0
     cycler: 0.10.0
     Cython: 0.29.23
     decorator: 4.4.2
     distlib: 0.3.1
     distro: 1.5.0
     docutils: 0.17.1
     filelock: 3.0.12
     funcparserlib: 0.3.6
     grako: 3.16.5
     h5py: 3.2.1
     html2text: 2020.1.16
     idna: 2.10
     ihm: 0.20
     imagecodecs: 2021.4.28
     imagesize: 1.2.0
     ipykernel: 5.5.5
     ipython: 7.23.1
     ipython-genutils: 0.2.0
     jedi: 0.18.0
     Jinja2: 2.11.3
     jupyter-client: 6.1.12
     jupyter-core: 4.7.1
     kiwisolver: 1.3.1
     line-profiler: 3.3.0
     lxml: 4.6.3
     lz4: 3.1.3
     MarkupSafe: 1.1.1
     matplotlib: 3.4.2
     matplotlib-inline: 0.1.2
     msgpack: 1.0.2
     netCDF4: 1.5.6
     networkx: 2.5.1
     numexpr: 2.7.3
     numpy: 1.20.3
     numpydoc: 1.1.0
     openvr: 1.16.801
     packaging: 20.9
     ParmEd: 3.2.0
     parso: 0.8.2
     pexpect: 4.8.0
     pickleshare: 0.7.5
     Pillow: 8.2.0
     pip: 21.1.1
     pkginfo: 1.7.0
     prompt-toolkit: 3.0.19
     psutil: 5.8.0
     ptyprocess: 0.7.0
     pycollada: 0.7.1
     pydicom: 2.1.2
     Pygments: 2.9.0
     PyOpenGL: 3.1.5
     PyOpenGL-accelerate: 3.1.5
     pyparsing: 2.4.7
     PyQt5-commercial: 5.15.2
     PyQt5-sip: 12.8.1
     PyQtWebEngine-commercial: 5.15.2
     python-dateutil: 2.8.1
     pytz: 2021.1
     pyzmq: 22.1.0
     qtconsole: 5.1.0
     QtPy: 1.9.0
     RandomWords: 0.3.0
     requests: 2.25.1
     scipy: 1.6.3
     setuptools: 57.0.0
     sfftk-rw: 0.7.0.post1
     six: 1.16.0
     snowballstemmer: 2.1.0
     sortedcontainers: 2.4.0
     Sphinx: 4.0.1
     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: 5.0.5
     urllib3: 1.26.5
     wcwidth: 0.2.5
     webcolors: 1.11.1
     wheel: 0.36.2
     wheel-filename: 1.3.0

 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/4881>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

comment:2 by Tom Goddard, 4 years ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Pseudobonds don't go to atom with ribbon when not hiding backbone atoms

comment:3 by Tom Goddard, 4 years ago

Cc: Eric Pettersen added
Resolution: → fixed
Status: assigned → closed

Fixed.

Atom::effective_coord() was giving the ribbon position even when ribbon hide backbone was false. I changed it to give the atom center position if ribbon is not hiding backbone atoms.

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