CA-only PDB not chained

[eugenejyuan@…]

Dear ChimeraX Development Team,

I hope this email finds you well. I am writing to bring an issue that I've encountered in the new ChimeraX version 1.7 to your attention.

With the previous versions, notably version 1.16.1, I have been able to render .pdb files that contain only CA atoms in a cartoon form. Unfortunately, I've noticed that this feature seems changed in the recent update. Now .pdb files with only CA atoms cannot be rendered as a cartoon. Interestingly, I've found out that saving the same content as .cif format allows one to be displayed as a ribbon.

An example is the .pdb file can be render as following before:

But now only atoms in version 1.7:

The attachment is the .pdb file I used to visulize in ChimeraX.

test.pdb​

I am wondering if this is a bug or an intentional design adjustment? To best understand how to proceed, I would truly appreciate if you could share your insights on this matter.

Thank you for your time and support, and I look forward to your reply.

Best regards,
Jing

[eugenejyuan@…]

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[eugenejyuan@…]

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[eugenejyuan@…]

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[Eric Pettersen]

Reported by Yuan Jing

[Eric Pettersen]

Hi Juan,

Thanks for reporting this problem and providing a test case. It is bug and not a deliberate change. I have fixed the bug and it will be in tomorrow's 1.8 daily build, and in a 1.7.1 if and when we make such a release.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

fix: ​https://github.com/RBVI/ChimeraX/commit/e258039c5dca3dbb0ed7fd9c57b88146ca8e555c

[eugenejyuan@…]

Dear Eric,

Thank you very much for your swift and efficient response.

Sincerely,
Jing

ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 于2023年12月22日周五 09:57写道：

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