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 <mailto:RKrishnan@BIOCRYST.com>> Subject: RE: Your message to chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> awaits moderator approval Date: November 25, 2025 at 8:19:02 AM PST To: "chimerax-users-bounces@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>" <chimerax-users-bounces@cgl.ucsf.edu <mailto:chimerax-users-bounces@cgl.ucsf.edu>>
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 CONFIDENTIALITY NOTICE
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