Duplicate residues created in Chain

[goddard@…]

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005121634 (2020-05-12 16:34:48 UTC)
Description
Saving mmcif writes out two copies of the same residue.
I open the 7bv2_extended.pdb written by Chimera 1.14, then save it as test.cif.  The single F86 residue (number 101) in the original PDB  becomes two F86 residues in the mmCIF (both numbered 101).

Log:
UCSF ChimeraX version: 1.0rc202005121634 (2020-05-12)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/goddard/ucsf/presentations/remdesivir-may2020/7bv2_extended.pdb
> format pdb

Chain information for 7bv2_extended.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
P | No description available  
T | No description available  
  

> select

8810 atoms, 9071 bonds, 17 pseudobonds, 3 models selected  

> save test.cif

Not saving entity_poly_seq for non-authoritative sequences  

> close

> open test.cif

Summary of feedback from opening test.cif  
---  
warnings | Unknown polymer entity '1' near line 115  
Unknown polymer entity '2' near line 6785  
Unknown polymer entity '3' near line 7641  
Unknown polymer entity '4' near line 8122  
Unknown polymer entity '5' near line 8553  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for test.cif #1  
---  
Chain | Description  
A | ?  
B | ?  
C | ?  
P | ?  
T | ?  
  

> select

8834 atoms, 9097 bonds, 19 pseudobonds, 3 models selected  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.100.362.0.0 (iBridge: 17.16.14281.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.4 (19E287)
      Kernel Version: Darwin 19.4.0
      Time since boot: 6 days 3:33

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      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
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: 7bv2_extended.pdb

7bv2_extended.pdb​

[goddard@…]

Added by email2trac

[Tristan Croll]

I've seen something like this before - but it was in the context of a severely flawed PDB file given to me where various residues had different atoms of the same name, so I didn't bother to report it.

[goddard@…]

This PDB file could have some "unique" features.  I made it with "combine" in Chimera 1.14 where I placed RNA oligomer in the same chain as 7bv2 /P with residue numbers starting one beyond a non-standard residue.  It seems ok to me and the ChimeraX PDB reader has no complaints about it.  But the mmCIF writer seems confused by it.

[Greg Couch]

This appears to be a bug in the PDB reader. If you list the residues in the chain, F86 appears twice.

m = session.models[0]
c = m.chains[3]
for r in c.residues:
  print(r.name)

And that causes the mmCIF write to output it twice.

[pett]

F86 can be polymeric, but its phosphorus is named P1, so loosened polymeric decision rules to allow for that.