Hi Krish,

  This is a known problem with Boltz, that it sometimes gets ligand geometry wrong.  There is nothing ChimeraX can do about this problem, and you should discuss it with Boltz developers via Boltz github issues

https://github.com/jwohlwend/boltz/issues

Here are some examples of existing issues about bad ligand geometry in Boltz

  wrong chirality - https://github.com/jwohlwend/boltz/issues/589

  wrong planarity - https://github.com/jwohlwend/boltz/issues/270

  wrong planarity - https://github.com/jwohlwend/boltz/issues/65

I have not read any suggested fixes for this.  The Boltz discussions identify that there appear to be problems in both identifying chiral centers and bond orders.

Tom



On Nov 25, 2025, at 10:36 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Begin forwarded message:

From: Krishnan Raman <RKrishnan@BIOCRYST.com>
Subject: RE: Your message to chimerax-users@cgl.ucsf.edu awaits moderator approval
Date: November 25, 2025 at 8:19:02 AM PST


Hi Guys,
This is about the behavior of smiles uploaded for boltz predictions. Some of the small molecule structures are incorrect after the predictions. My cyclohexyl ring was flattened to a benzene like ring; my protonated amine group in a benzyl amine ended up looking like a cyano group. Anything we can do about it?
Thanks
Krish

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