Hi Arun, Here is the "boltz predict" command help, which you could also see from using ChimeraX command "help boltz predict": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/boltz.html#predict> The syntax is shown in the Usage line. Your command is wrong because: (1) you should not include the word "sequences" which would be replaced with the actual sequence(s) (2) there is no "nstruct" option (3) there is no "steering" option I don't know where you saw those options, maybe you are looking in some other documentation that is not for ChimeraX. So anyway you'd want something like boltz predict protein MKALTQRPLD[...rest of sequence...] recycles 10 How to specify "sequences" including multiple sequences is explained in the documentation link above. There are a few different ways so I'll let you read it there instead of repeating it all here. For a specific example, see also the following page and the video on this topic. <https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/boltz_help.html> <https://www.youtube.com/watch?v=377V9A_0ECc> I hope this helps, 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 Jun 20, 2025, at 2:18 AM, Arun Gupta via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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
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