Spurious TER cards

[claudia.kielkopf@…]

The following bug report has been submitted:
Platform:        macOS-14.3-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Dear Chimerax team,

I'm puzzled over a behaviour of Chimerax 1.7/ISOLDE that wasn't there when I was still using 1.6.1. I've been refining a structure in 1.6.1 where there are some loops/areas deleted due to bad density. I now took model building up in 1.7 again, starting from a phenix refinement that took a pdb saved from 1.6.1 as input, no errors from Chimerax/ISODLE, didn't notice anything different. But when I refined this newly manually built model in phenix 1.21rc, the refinement runs fine, but there is no cablam validation for chain D which is the one that has some loops deleted. I checked the pdb file I saved in 1.7 after ISOLDE rebuild, it looks like 1.7 puts a TER record at all areas that are missing (that's new to me), but funnily enough, 1.7 doesn't show the broken lines that it usually would in the areas where there's a stretch/loop missing. Someone told me there's a difference in the way 1.7 handles SEQRES, so I deleted the SEQRES lines and the TER wihtin the chain D from the pdb file manually before refining in phenix, and then the cablam validation is as it should. I can't find anything in the change log for 1.7 or in the mailing list, which is why I'm so confused as to what exactly is going on. It's impacting phenix validation and it's also confusing if chimerax 1.7 all of a sudden doesn't show the broken lines for deleted residues in some pdb files that I refined before. Maybe there's a simple explanation for this, so I'd love to hear from you. I'm happy to provide phenix screenshots and pdb files (confidentially) if this helps you to recreate the problem. Thank you in advance, ChimeraX is one of the best programs I'm using on a daily basis, so thank you for your hard work.

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 6roa

6roa title:  
Crystal structure of V57G mutant of human cystatin C [more info...]  
  
Chain information for 6roa #1  
---  
Chain | Description | UniProt  
A B | Cystatin-C | CYTC_HUMAN 1-120  
  
6roa mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> open 6rao

6rao title:  
Cryo-EM structure of the anti-feeding prophage (AFP) baseplate, 6-fold
symmetrised [more info...]  
  
Chain information for 6rao #2  
---  
Chain | Description | UniProt  
A B | Afp1 | Q6HAD8_9GAMM 1-149  
C | Afp2 | Q6HAD7_9GAMM 1-354  
D | Afp3 | Q6HAD6_9GAMM 1-451  
E | Afp4 | Q6HAD5_9GAMM 1-417  
F | Afp5 | Q6HAD4_9GAMM 1-149  
G | Afp7 | Q6HAD2_9GAMM 1-229  
H | Afp9 | Q6HAD0_9GAMM 1-140  
I | Afp11 | Q6HAC8_9GAMM 1-605  
J | Afp12 | Q6HAC7_9GAMM 1-963  
  
6rao mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> close #1

> hide atoms

> show cartoons

> close session

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp13/Afp12-13_locrec/RealSpaceRefine_15/Afp13_12ref_refined_010_cablamtry4_test_delseqres_real_space_refined_015.pdb

Chain information for
Afp13_12ref_refined_010_cablamtry4_test_delseqres_real_space_refined_015.pdb
#1  
---  
Chain | Description  
A B C | No description available  
D | No description available  
  

> open
> /Users/mvc492/Documents/Results/Modelbuilding/Afp13/Afp12-13_locrec/RealSpaceRefine_10/Afp13_12ref_refined_007_real_space_refined_010.pdb

Chain information for Afp13_12ref_refined_007_real_space_refined_010.pdb #2  
---  
Chain | Description  
A B C | No description available  
D | No description available  
  




OpenGL version: 4.1 INTEL-22.1.29
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 2020.80.5.0.1 (iBridge: 21.16.3049.0.0,0)
      OS Loader Version: 580~1337

Software:

    System Software Overview:

      System Version: macOS 14.3 (23D56)
      Kernel Version: Darwin 23.3.0
      Time since boot: 7 hours, 52 minutes

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        P27q-20:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: V905LK6Wÿÿÿÿ
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.55


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    ChimeraX-gltf: 1.0
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[Eric Pettersen]

Hi Claudia,

Thanks for reporting this problem. The TER cards that 1.7 wrote were incorrect (should have been omitted) and cause the lack of missing-structure pseudobonds when you open that PDB. This behavior has been fixed in the 1.7.1 release, so please use that instead.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab