Dear ChimeraX Team,

I'm currently working with the Boltz structure prediction tool in ChimeraX GUI (ChimeraX 1.10 Release Candidate (15 June 2025) ) and would appreciate your guidance on the correct command syntax—particularly when specifying the single or multiple protein components via the ChimeraX GUI command line.

I would like to run Boltz predictions with the following specific parameters:

nstruct: 5 (Default is 1)
recycles: 10 (Default is 3)
seed: 42 (Random numbers of seed (integer), Fixed seed value ensures reproducible results)
steering: true (enables or disables the steering potential)

I tried running the following command in the command line, "boltz predict protein sequences "MKALTQRPLD... (your protein sequence)" nstruct 5 recycles 10 steering true" but it doesn't work.

Could you please provide an example of the correct command format for:

A single molecular component (e.g., one protein sequence).
A multi-component system (e.g., protein + peptide or multiple protein chains).

Additionally, if there are any special considerations or formatting requirements for specifying multiple sequences or components in the GUI , I’d be grateful for your advice.

Thank you for your time and support.

Best Regards,

Arun

Arun Gupta PhD, MRSC

Sr. Post Doctoral Research Assistant

Gillespie/McMichael Group

Nuffield Dept. of Clinical Medicine,

University of Oxford,

Centre for Immuno-Oncology

Old Road Campus Research Building,

Roosevelt Drive, Oxford

OX3 7DQ

Tel: + 44 (0)1865 2612913