(pseudo)bonds in X3D output do not connect to ribbon

[phil.cruz@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202012160251 (2020-12-16 02:51:00 UTC)
Description
Saving .x3d files using the cx_unified.py script for NIH 3D produces .x3d files where the struts and hydrogen bonds don't connect to the ribbons properly.  Attached is the ChimeraX session file that was saved right after writing the first set of output files for the color by secondary structure representation.  Note that the .glb file seems to be okay.

Let me know if you want the .x3d file that is produced. 

Log:
UCSF ChimeraX version: 1.2.dev202012160251 (2020-12-16)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> cd ..

Current working directory is: /Users/cruzp2  

> cd sandbox

Current working directory is: /Users/cruzp2/sandbox  

> runscript "/Users/cruzp2/OneDrive - National Institutes of
> Health/NIH3D/code/nih-3d-resource-
> workflows/chimera_x_scripts/cx_unified_bug.py" --pdb 2hhb

> open pdbe_bio:2HHB autoStyle false

Summary of feedback from opening 2HHB fetched from pdbe_bio  
---  
warning | Missing or incomplete entity_poly_seq table. Inferred polymer
connectivity.  
  
2HHB bioassembly 1 title:  
The crystal structure of human deoxyhaemoglobin At 1.74 angstroms resolution
[more info...]  
  
Chain information for 2HHB bioassembly 1 #1  
---  
Chain | Description  
A C | hemoglobin (deoxy) (α chain)  
B D | hemoglobin (deoxy) (β chain)  
  
Non-standard residues in 2HHB bioassembly 1 #1  
---  
HEM — (HEM)  
PO4 — (PO4)  
  
Opened 1 biological assemblies for 2HHB  

> windowsize 512 512

> graphics bgColor white

> color name marine 0,50,100

Color 'marine' is opaque, 0% red, 50% green, and 100% blue

  

> color name forest 13.3,54.5,13.3

Color 'forest' is opaque, 13.3% red, 54.5% green, and 13.3% blue

  

> color name tangerine 95.3,51.8,0

Color 'tangerine' is opaque, 95.3% red, 51.8% green, and 0% blue

  

> color name grape 64.3,0,86.7

Color 'grape' is opaque, 64.3% red, 0% green, and 86.7% blue

  

> color name nih_blue 12.5,33.3,54.1

Color 'nih_blue' is opaque, 12.5% red, 33.3% green, and 54.1% blue

  

> color name jmol_carbon 56.5,56.5,56.5

Color 'jmol_carbon' is opaque, 56.5% red, 56.5% green, and 56.5% blue

  

> color name bond_purple 57.6,43.9,85.9

Color 'bond_purple' is opaque, 57.6% red, 43.9% green, and 85.9% blue

  

> color name struts_grey 48,48,48

Color 'struts_grey' is opaque, 48% red, 48% green, and 48% blue

  

> color name carbon_grey 22.2,22.2,22.2

Color 'carbon_grey' is opaque, 22.2% red, 22.2% green, and 22.2% blue

  

> delete solvent

> delete H

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> wait 1

> nucleotides ladder radius 1.2

> select backbone & protein | nucleic-acid & sel | ions | ligand | ligand :< 5
> & ~nucleic-acid

2300 atoms, 2296 bonds, 574 residues, 1 model selected  

> hbonds sel color white restrict both

417 hydrogen bonds found  

> struts @ca|ligand|P|##num_atoms<500 length 8 loop 60 radius 0.75 color
> struts_grey

Created 46 struts for @ca | ligand | P | ##num_atoms<500, max length 8, max
loop length 60  
  

> ~struts @PB,PG

> ~struts adenine|cytosine|guanine|thymine|uracil

> color white

> color helix marine

> color strand firebrick

> color coil goldenrod

> color nucleic-acid forest

> color :A:C:G:U grape

> color byatom

> select C & ligand | C & ligand :< 5 &~nucleic-acid| C & protein| C &
> disulfide

658 atoms, 580 bonds, 12 pseudobonds, 89 residues, 2 models selected  

> color sel carbon_grey atoms

> color ligand|protein&sideonly byhetero atoms

> ~select

Nothing selected  

> color struts_grey pseudobonds

> size stickRadius 0.8

Changed 4684 bond radii  

> style dashes 0

Changed 3 pseudobond dashes  

> size pseudobondRadius 0.6

Changed 479 pseudobond radii  

> save 2HHB-ribbon-secondary.png width 512 height 512 supersample 3

> save 2HHB-ribbon-secondary.glb

> save 2HHB-ribbon-secondary.x3d

> save 2HHB-ribbon-secondary.stl

> save /Users/cruzp2/sandbox/strut_x3d_bug.cxs




OpenGL version: 4.1 ATI-2.11.23
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro14,3
      Processor Name: Intel Core i7
      Processor Speed: 3.1 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 429.80.1.0.0
      SMC Version (system): 2.45f0

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G8022)
      Kernel Version: Darwin 18.7.0
      Time since boot: 3 days 2:01

Graphics/Displays:

    Intel HD Graphics 630:

      Chipset Model: Intel HD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x591b
      Revision ID: 0x0004
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro 560:

      Chipset Model: Radeon Pro 560
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c0
      ROM Revision: 113-C980AJ-927
      VBIOS Version: 113-C9801AU-A02
      EFI Driver Version: 01.A0.927
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.29 [3.2.8]
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
        BenQ GW2750H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 6CD03450SL0 
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55
        D32hn-D0:
          Resolution: 1366 x 768 (WSGA - Wide eXtended Graphics Array)
          UI Looks like: 1366 x 768 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: LAUFUKBR00000
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: Apple USB-C Digital AV Adapter
          Automatically Adjust Brightness: No
          Adapter Firmware Version: 2.35

Locale: (None, 'UTF-8')
PySide2 version: 5.15.2
Qt version: 5.15.2
Installed Packages:
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    certifi: 2020.12.5
    cftime: 1.3.0
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
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    ChimeraX-Core: 1.2.dev202012160251
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    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
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    ChimeraX-Movie: 1.0
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File attachment: strut_x3d_bug.cxs

strut_x3d_bug.cxs​

[phil.cruz@…]

Added by email2trac

[Greg Couch]

Was able to reproduce this with 1gcn, a helix, and the command "hbond dashes 0". The saved X3D output had the hbonds disconnected from the ribbon.

It is fixed now.