Hi Xicong,

  As Elaine said ChimeraX does not currently have a user interface to modify residues in Boltz predictions.  I have not had time to add that yet.  But you can pretty easily add the modification to input file for Boltz that ChimeraX creates and run it from a terminal.

  Here is an example of how to predicted a protein with a phosphoserine, I used PDB 2PIL as an example.  I ran Boltz in ChimeraX with a standard serine.  Here is the input YAML file ChimeraX produced ~/Desktop/2pil/2pil.yaml

version: 1
sequences:
  - protein:
      id: [A]
      sequence: FTLIELMIVIAIVGILAAVALPAYQDYTARAQVSEAILLAEGQKSAVTEYYLNHGKWPENNTSAGVASPPSDIKGKYVKEVEVKNGVVTATMLSSGVNNEIKGKKLSLWARRENGSVKWFCGQPVTRTDDDTVADAKDGKEIDTKHLPSTCRDNFDAK

I copied this 2pil.yaml file to 2pil_sep.yaml and added a few lines to say make serine 68 a phosphoserine (3-letter code SEP):

version: 1
sequences:
  - protein:
      id: [A]
      sequence: FTLIELMIVIAIVGILAAVALPAYQDYTARAQVSEAILLAEGQKSAVTEYYLNHGKWPENNTSAGVASPPSDIKGKYVKEVEVKNGVVTATMLSSGVNNEIKGKKLSLWARRENGSVKWFCGQPVTRTDDDTVADAKDGKEIDTKHLPSTCRDNFDAK
      modifications:
        - position: 68
          ccd: SEP

Then I reran the boltz command that ChimeraX used from a terminal changing the 2pil.yaml input file to 2pil_sep.yaml.  The command ChimeraX used is in the ~/Desktop/2pil/command file

$ /Users/goddard/boltz/bin/boltz predict /Users/goddard/Desktop/boltz/boltz_2pil/2pil_sep.yaml --write_full_pae --use_msa_server --accelerator gpu --no_potentials

When that ran it put the resulting predictions in

boltz_results_2pil_sep/predictions/2pil_sep/2pil_sep_model_0.cif

so I open that prediction in ChimeraX and aligned it to my original PDB using ChimeraX command "matchmaker #3 to #1".  Result is shown in the image below.  The Boltz documentation page shows other ways you can modify the input .yaml file for instance to add templates or constraints between atoms

https://github.com/jwohlwend/boltz/blob/main/docs/prediction.md

In the future I hope to provide ChimeraX user interfaces to allow those possibilities.

  Tom

PDB 2PIL in tan, Boltz prediction with serine 68 in blue, Boltz prediction with phosposerine 68 in pink.

boltz_mod.png

On Aug 7, 2025, at 8:36 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Sorry no, the ChimeraX tool to run Boltz does not have a way to define post-translational modifications. This issue is mentioned in the Limitations section:

<https://rbvi.ucsf.edu/chimerax/docs/user/tools/boltz.html#limitations>

Best regards,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 6, 2025, at 7:07 PM, Xicong Wang via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX developers,
I'm trying to predict a structure with two phosphorylated residues using Boltz. Is there an option for me to do that in ChimeraX? I didn't find any options to let me do any post-translational modification on the protein sequence I entered.
Best regards,
Xicong Wang


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