Incorrect ring pyridine protonation

[jonipsaro@…]

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.10rc202505300032 (2025-05-30 00:32:35 UTC)
Description
The addh command is incorrectly adding a proton to certain small molecules.  In my case it is reproducibly protonating the N in pyridine rings.  This is only happening when I use this 1.10 version.  When going back to 1.7.1, addh is behaving correctly.  Thanks for all your work!

OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac15,11
      Model Number: MRW33LL/A
      Chip: Apple M3 Max
      Total Number of Cores: 14 (10 performance and 4 efficiency)
      Memory: 36 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 28 days, 3 hours, 26 minutes

Graphics/Displays:

    Apple M3 Max:

      Chipset Model: Apple M3 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 30
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL P2422HE:
          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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[pett]

Hi Jon,

I cannot reproduce this with the structures I've tried. For instance, niacin (open pubchem:938) does not get a proton on the ring nitrogen when hydrogens are added. Perhaps you could share a PubChem code, CCD identifier, or SMILES string that reproduces the problem?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[jonipsaro@…]

Hi Eric,

Thanks for the quick response!

Attached you'll find:
1. A pdb file that has a clipping of a compound (rings2.pdb).
2. A screenshot from v.1.7
3. A screenshot from v.1.10

For both versions, I just opened the pdb file and issued the addh command.
Maybe I'm overlooking something?

Keep me posted and thanks again,
Jon


On 7/9/25, 8:04 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:


#18158: Incorrect ring pyridine protonation
----------------------------------------+----------------------
Reporter: jonipsaro@… | Owner: pett
Type: defect | Status: feedback
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+----------------------
Changes (by pett):


* status: accepted => feedback


Comment:


Hi Jon,
I cannot reproduce this with the structures I've tried. For
instance, niacin (open pubchem:938) does not get a proton on the ring
nitrogen when hydrogens are added. Perhaps you could share a PubChem
code, CCD identifier, or SMILES string that reproduces the problem?


--Eric


Eric Pettersen
UCSF Computer Graphics Lab
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18158#comment:2> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18158#comment:2&gt;>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/&gt;>
ChimeraX Issue Tracker




________________________________

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rings2.pdb​

v.1.7.png​

v1.10.png​

[jonipsaro@…]

Added by email2trac

[jonipsaro@…]

Added by email2trac

[jonipsaro@…]

Added by email2trac

[pett]

I find that with your structure, ChimeraX 1.10 sometimes adds a proton to the N and sometimes it doesn't (i.e. sometimes assigns it atom type N2 and sometimes Npl). Obviously that's a bug, but might explain why I had trouble reproducing the problem.

[jonipsaro@…]

Thanks, Eric.

Any recommendation for me?
I can just use 1.7 unless you think there is something I can specify (either in the PDB file or in ChimeraX).

Jon

\ufeffOn 7/10/25, 2:37 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:


#18158: Incorrect ring pyridine protonation
----------------------------------------+----------------------
Reporter: jonipsaro@\u2026 | Owner: pett
Type: defect | Status: accepted
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+----------------------
Changes (by pett):


* status: feedback => accepted


Comment:


I find that with your structure, ChimeraX 1.10 sometimes adds a proton to
the N and sometimes it doesn't (i.e. sometimes assigns it atom type N2 and
sometimes Npl). Obviously that's a bug, but might explain why I had
trouble reproducing the problem.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18158#comment:4> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18158#comment:4&gt;>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/&gt;>
ChimeraX Issue Tracker




________________________________

CONFIDENTIALITY NOTICE: This communication may contain privileged, confidential and/or sensitive information and is intended only for the party to whom it is addressed and for the stated purpose. If you are not its intended recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation to the contents of this communication is strictly prohibited and may be unlawful. If you have received this message in error, please notify the sender and then immediately delete it without reading its contents.

[pett]

I'm investigating it right now, but you can force the correct protonation by selecting the ring nitrogen and then issuing the command "setattr sel a idatm_type N2" before adding hydrogens.

[jonipsaro@…]

Awesome. Thanks for the tip!

\ufeffOn 7/10/25, 3:52 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:


#18158: Incorrect ring pyridine protonation
----------------------------------------+----------------------
Reporter: jonipsaro@\u2026 | Owner: pett
Type: defect | Status: accepted
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+----------------------
Comment (by pett):


I'm investigating it right now, but you can force the correct protonation
by selecting the ring nitrogen and then issuing the command "setattr sel a
idatm_type N2" before adding hydrogens.
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18158#comment:6> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18158#comment:6&gt;>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/&gt;>
ChimeraX Issue Tracker




________________________________

CONFIDENTIALITY NOTICE: This communication may contain privileged, confidential and/or sensitive information and is intended only for the party to whom it is addressed and for the stated purpose. If you are not its intended recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation to the contents of this communication is strictly prohibited and may be unlawful. If you have received this message in error, please notify the sender and then immediately delete it without reading its contents.

[pett]

Fixed. Fix will be in tomorrow's daily build and in the upcoming 1.10.1 release (which might be a week or two).

Fix: ​https://github.com/RBVI/ChimeraX/commit/e52e03672a827a868342ca8326d128705094ebdf

[jonipsaro@…]

Awesome.  Speedy work!  Appreciate it.
Jon

\ufeffOn 7/10/25, 4:48 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu <mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:


#18158: Incorrect ring pyridine protonation
----------------------------------------+--------------------
Reporter: jonipsaro@\u2026 | Owner: pett
Type: defect | Status: closed
Priority: normal | Milestone:
Component: Structure Editing | Version:
Resolution: fixed | Keywords:
Blocked By: | Blocking:
Notify when closed: | Platform: all
Project: ChimeraX |
----------------------------------------+--------------------
Changes (by pett):


* resolution: => fixed
* status: accepted => closed


Comment:


Fixed. Fix will be in tomorrow's daily build and in the upcoming 1.10.1
release (which might be a week or two).


Fix:
https://github.com/RBVI/ChimeraX/commit/e52e03672a827a868342ca8326d128705094ebdf <https://github.com/RBVI/ChimeraX/commit/e52e03672a827a868342ca8326d128705094ebdf>
--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18158#comment:8> <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/18158#comment:8&gt;>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/> <https://www.rbvi.ucsf.edu/chimerax/&gt;>
ChimeraX Issue Tracker




________________________________

CONFIDENTIALITY NOTICE: This communication may contain privileged, confidential and/or sensitive information and is intended only for the party to whom it is addressed and for the stated purpose. If you are not its intended recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation to the contents of this communication is strictly prohibited and may be unlawful. If you have received this message in error, please notify the sender and then immediately delete it without reading its contents.