USE CAUTION: External Message.

Hi Radhika,

  Elaine is right.  You are probably using ChimeraX 1.10 from June 2025 and Boltz ligand affinity prediction came out after that release.  So you need to get a current ChimeraX release candidate or daily build to predict affinity.  Also the affinity should not be treated as a real Kd value, it is just a qualitative score.

  Here is what a prediction with ligand affinity looks like in the ChimeraX daily build.  The log reports the affinity as 36 uM and also has the "open" command which shows where the data is located on your computer, in this example,

        open /Users/goddard/Desktop/boltz/boltz_8rf4_98/boltz_results_8rf4/predictions/8rf4/8rf4_model_0.cif

A text file with confidence scores will be found in the same directory.

        Tom

<boltz_affinity.png>

> On Dec 4, 2025, at 12:51 PM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>
> Hi Radhika,
> Maybe you are using an older version.  The current version of the Boltz tool (in ChimeraX 1.11 since July 22, 2025) has an option "Predict ligand binding affinity..." and I do not see that in your image, so maybe there isn't any such prediction in your results.  See current help pages:
>
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__rbvi.ucsf.edu_chimerax_docs_user_tools_boltz.html-23dialog&d=DwIFaQ&c=shNJtf5dKgNcPZ6Yh64b-ALLUrcfR-4CCQkZVKC8w3o&r=aXNKhe55pvtfwzZJ15wwcWO9f_JSWzzBBdLWTnYrla8&m=18a4YvwSzNoc8QRJN9gQjiNo316JyPorMhBtiyOeXMtpvkIYyVUmx57HUeprI1CD&s=fwU8QiV4Ot6zFCXA9Idtz7fw6pnJPmqum2n3o-GwXbE&e= >
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.rbvi.ucsf.edu_chimerax_data_boltz-2Dapr2025_boltz-5Fhelp.html&d=DwIFaQ&c=shNJtf5dKgNcPZ6Yh64b-ALLUrcfR-4CCQkZVKC8w3o&r=aXNKhe55pvtfwzZJ15wwcWO9f_JSWzzBBdLWTnYrla8&m=18a4YvwSzNoc8QRJN9gQjiNo316JyPorMhBtiyOeXMtpvkIYyVUmx57HUeprI1CD&s=mZsFI0nl7VLyfllDMZwVVLz46IH8rDeID0HOKSbDYDU&e= >
>
> So you may need to get ChimeraX 1.11 and rerun your calculation with the option turned on to get the affinity prediction.
>
> Regards,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Dec 4, 2025, at 10:54 AM, Malik, Radhika via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
>>
>> Hello,
>>
>> I am a Research Scientist at Mount Sinai School of Medicine, NY.   I have run Boltz in ChimeraX on a protein-ligand complex, however, I am not able to locate the file for the predicted Kd values. Can you please direct me to the file/location? I am attaching a screenshot of what I see after the run.
>>
>> Thanks a lot,
>> Radhika
>> <Screenshot 2025-12-04 at 1.52.02 PM.png>
>
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