internscience Chroma Protein Generation Toolkit
Note:
- Local files are not directly accessible by the server. Please upload them to the server using
molclaw-file-transferbefore execution. - For PDB file inputs, it is recommended to preprocess them using
molclaw-pdbfixerbefore execution. - Please refer to skill
molclaw-scp-serverto complete tool invocation.
Usage
1. Monomer Protein Generation
The description of tool chroma_monomer.
Generates a de novo single-chain protein candidate for exploratory protein design workflows.
Args:
length (int): Number of residues in the monomer chain. Default: 100.
steps (int): Diffusion sampling step count. Default: 500.
device (str): Chroma execution device string. Default: 'cuda:0'.
fmt (str): Output structure format, one of {'cif', 'pdb'}. Default: 'cif'.
api_key (str|None): Optional Chroma API key for model access.
dry_run (bool): If True, validate parameters and prepare output paths without model sampling. Default: False.
Return:
status (str): 'success' or 'error'.
msg (str): Human-readable execution summary.
tool_name (str): Tool identifier 'chroma_monomer'.
output_dir (str): Run-specific output directory under tool_result/chroma_toolkit_result.
output_file (str): Target output structure file path.
length (int): Effective residue length used in generation.
steps (int): Effective sampling steps used in generation.
device (str): Effective execution device.
format (str): Effective output format.
How to use tool chroma_monomer :
response = await client.session.call_tool(
"chroma_monomer",
arguments={
"length": 150,
"steps": 500,
"device": "cuda:0",
"fmt": "cif",
"dry_run": False
}
)
result = client.parse_result(response)
output_file = result["output_file"]
Example parameter sets
# 1) Main mode
{
"length": 150,
"steps": 500,
"device": "cuda:0",
"fmt": "cif",
"dry_run": False
}
# 2) Variant mode
{
"length": 100,
"steps": 50,
"fmt": "cif",
"dry_run": True
}
2. Complex Protein Generation
The description of tool chroma_complex.
Generates a multi-chain protein complex candidate for interface and assembly design studies.
Args:
chains (str): Comma-separated chain lengths, for example '100,120'. Default: '100,100'.
steps (int): Diffusion sampling step count. Default: 500.
device (str): Chroma execution device string. Default: 'cuda:0'.
fmt (str): Output structure format, one of {'cif', 'pdb'}. Default: 'cif'.
api_key (str|None): Optional Chroma API key for model access.
dry_run (bool): If True, validate parameters and prepare output paths without model sampling. Default: False.
Return:
status (str): 'success' or 'error'.
msg (str): Human-readable execution summary.
tool_name (str): Tool identifier 'chroma_complex'.
output_dir (str): Run-specific output directory under tool_result/chroma_toolkit_result.
output_file (str): Target output structure file path.
chains (str): Effective chain-length specification used in generation.
steps (int): Effective sampling steps used in generation.
device (str): Effective execution device.
format (str): Effective output format.
How to use tool chroma_complex :
response = await client.session.call_tool(
"chroma_complex",
arguments={
"chains": "100,120",
"steps": 500,
"device": "cuda:0",
"fmt": "cif",
"dry_run": False
}
)
result = client.parse_result(response)
output_file = result["output_file"]
Example parameter sets
# 1) Main mode
{
"chains": "100,120",
"steps": 500,
"device": "cuda:0",
"fmt": "cif",
"dry_run": False
}
# 2) Variant mode
{
"chains": "80,80,80",
"steps": 50,
"fmt": "pdb",
"dry_run": True
}
3. Symmetry-Constrained Protein Generation
The description of tool chroma_symmetry.
Generates a symmetry-constrained protein design candidate for oligomeric architecture exploration.
Args:
group (str): Symmetry group label such as 'C_3' or 'D_2'.
length (int): Residue count per protomer chain. Default: 100.
steps (int): Diffusion sampling step count. Default: 500.
num_chain_neighbors (int): Neighbor-chain count for symmetry conditioner. Default: 2.
langevin_factor (float): Langevin factor for conditioned sampling. Default: 8.0.
inverse_temperature (float): Inverse temperature for conditioned sampling. Default: 8.0.
device (str): Chroma execution device string. Default: 'cuda:0'.
fmt (str): Output structure format, one of {'cif', 'pdb'}. Default: 'cif'.
api_key (str|None): Optional Chroma API key for model access.
dry_run (bool): If True, validate parameters and prepare output paths without model sampling. Default: False.
Return:
status (str): 'success' or 'error'.
msg (str): Human-readable execution summary.
tool_name (str): Tool identifier 'chroma_symmetry'.
output_dir (str): Run-specific output directory under tool_result/chroma_toolkit_result.
output_file (str): Target output structure file path.
group (str): Effective symmetry group used in generation.
length (int): Effective residue length per chain.
steps (int): Effective sampling step count.
num_chain_neighbors (int): Effective neighbor-chain parameter.
langevin_factor (float): Effective Langevin factor.
inverse_temperature (float): Effective inverse temperature.
device (str): Effective execution device.
format (str): Effective output format.
How to use tool chroma_symmetry :
response = await client.session.call_tool(
"chroma_symmetry",
arguments={
"group": "C_3",
"length": 80,
"steps": 500,
"num_chain_neighbors": 2,
"langevin_factor": 8.0,
"inverse_temperature": 8.0,
"device": "cuda:0",
"fmt": "cif",
"dry_run": False
}
)
result = client.parse_result(response)
output_file = result["output_file"]
Example parameter sets
# 1) Main mode
{
"group": "C_3",
"length": 80,
"steps": 500,
"num_chain_neighbors": 2,
"langevin_factor": 8.0,
"inverse_temperature": 8.0,
"device": "cuda:0",
"fmt": "cif",
"dry_run": False
}
# 2) Variant mode
{
"group": "D_2",
"length": 100,
"steps": 50,
"num_chain_neighbors": 3,
"langevin_factor": 6.0,
"inverse_temperature": 10.0,
"fmt": "pdb",
"dry_run": True
}