Peptide not circular

[risa.shibuya@…]

The following bug report has been submitted:
Platform:        macOS-12.4-arm64-arm-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
I couldn't connect N-termini and C-termini of cyclized proteins in cartoon view or all atom view in ChimeraX.
In Chimera, it is possible to connect the N-termini and C-termini of cyclized proteins by adding the line of LINK to PDB.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/risa/Downloads/5ZO6_circ.pdb format pdb

5ZO6_circ.pdb title:  
Crystal structure of C166, A backbone circularized G-CSF [more info...]  
  
Chain information for 5ZO6_circ.pdb #1  
---  
Chain | Description | UniProt  
X | granulocyte colony-stimulating factor | CSF3_HUMAN 1-166  
  

> show atoms

> show sidechain target ab

> hide cartoons

> show cartoons

> hide cartoons

> hide atoms

> show atoms

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> set bgColor white

> show atoms

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> hide cartoons

> show cartoons

> ui mousemode right "link markers"

> ui mousemode right "mark maximum"

> ui mousemode right "mark plane"

> ui mousemode right "mark surface"

> open /Users/risa/Downloads/5ZO6_circ.pdb format pdb

5ZO6_circ.pdb title:  
Crystal structure of C166, A backbone circularized G-CSF [more info...]  
  
Chain information for 5ZO6_circ.pdb #2  
---  
Chain | Description | UniProt  
X | granulocyte colony-stimulating factor | CSF3_HUMAN 1-166  
  

> style stick

Changed 2722 atom styles  

> style stick

Changed 2722 atom styles  

> style stick

Changed 2722 atom styles  

> show atoms

> show sidechain target ab

> hide cartoons

> rainbow

> color byhetero




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 7459.121.3
      OS Loader Version: 7459.121.3

Software:

    System Software Overview:

      System Version: macOS 12.4 (21F79)
      Kernel Version: Darwin 21.5.0
      Time since boot: 93 days 2:04

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
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          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        RDT235WLM:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


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[Eric Pettersen]

Hi Risa,
	Only consecutive amino acids (with no intervening TER card and with the same chain ID) are implicitly connected in PDB format.  The circularizing bond needs to be specified by a LINK record.  When I supply the proper LINK record, the circularizing bond is created properly in ChimeraX, though you can only see it when viewing all atoms, since the cartoon depiction will still have a break in it.  The cartoon issue is a bug.  I will add you to recipient list for the ticket we have open for that so that you will be notified when it gets fixed.
	I have attached an edited PDB file with the proper LINK record.  I see that you are the author of the 5ZO6 entry, so you could possibly submit a revision that includes the LINK record (or the mmCIF equivalent).

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

circular.LINK.pdb​

[Eric Pettersen]

Added by email2trac

[risa.shibuya@…]

Dear Eric Pettersen

Thank you for your prompt reply.
Thank you also for sending the file with LINK record.
As you said, I could show the circularized bond by LINK record in ChimeraX.

The figure created by ChimeraX are great (in particular, I like “Soft”). So I'm using ChimeraX to create figures including 5ZO6 within the paper I plan to submit.
I am looking forward to seeing it in the cartoon as well.

******************************************************
Risa SHIBUYA, Ph.D.
Osaka University
Mail: risa.shibuya@bio.eng.osaka-u.ac.jp
******************************************************

[Eric Pettersen]

I'm glad you're enjoying ChimeraX! Unfortunately, it might be awhile before the broken-cartoon problem gets fixed.