Fwd: Boltz predictions and SMILES
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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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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:
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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
This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.
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participants (2)
-
Eric Pettersen -
Tom Goddard