X Openai Boltz Protein Screen 82c7642

---
name: x-openai-boltz-protein-screen-82c7642
description: Screen existing protein binders with Boltz. Use when ranking a supplied protein, peptide, antibody, nanobody, or binder library against a target. Not for designing new proteins or screening small molecules.
---

### 导出副本边界与技能别名

迁移、安装、修复和经验回写只作用于当前加载的目标宿主技能副本。原 Codex 技能/MCP、下载的源码和 `original-skills` 均为来源材料，不因执行本副本而写入；只有用户另行明确要求配置 Codex 产品本身时，才按该产品流程处理指定目标。脚本需要安装目录或状态目录时，显式提供目标路径；不得从 `CODEX_HOME` 隐式推断写入位置。

跨技能名称可能沿用源库别名。先查 [技能别名表](../../skill-aliases.json)，优先选择同来源、同插件的条目，再使用其 `id` 调用或读取对应入口；不得假定旧 `$skill`、`superpowers:skill` 名称在新宿主直接注册。不能确定目标时先核对，不替换真实产品命令或 Shell 环境变量。

## 跨宿主使用约定

本副本供支持 Agent Skills 的客户端使用。先检查当前宿主实际提供的工具、权限和已连接服务，再执行正文工作流。原文中的宿主工具标识是能力参考；只有实际发现该工具时才可调用，其他宿主应使用经核验的等价 MCP、CLI 或 API。没有等价能力的步骤必须报告不可用，不能虚构调用或完成状态。

技能资源以本技能目录为基准；输出写入当前项目中用户指定的位置。通过技能名称或自然语言触发，具体快捷命令由宿主决定。涉及真实产品、模型 API、协议字段和官方网址的名称保持原意。授权、审批、隐私和工具范围限制在迁移后仍然有效；不得为兼容而扩大权限。具体依赖与迁移说明见同目录 `PORTABILITY.md`。

## Workflow

If `boltz-api` is missing from `PATH`, use `boltz-cli-setup` for install/update guidance before retrying.
If a command reports missing or expired authentication, use `boltz-cli-setup` to start `boltz-api auth login --device-code` before retrying; do not ask permission first.
If the agent host sandbox blocks `boltz-api` install/auth/API calls, use `boltz-cli-setup` to request the host sandbox bypass/escalation needed for user-wide CLI install, browser login, credential storage, temp files, or API access before retrying.

Use this skill when the user already has candidate proteins / peptides / antibodies / nanobodies.

1. Normalize the binder library into `proteins` — a list of candidate complexes. For a simple sequence library each entry has one protein entity; multi-chain candidates (antibody heavy+light) are also allowed.
2. Pick the target variant:
   - `structure_template` — user has a CIF/PDB file or URL; select which chains are polymer vs ligand, which residues to keep (`crop_residues`), and optionally `epitope_residues` / `flexible_residues`.
   - `no_template` — user has only sequences; pass them as `target.entities` plus optional `epitope_residues`.
3. Don't add `bonds` / `constraints` unless the user asks for geometry constraints.
4. Author the payload YAML or JSON, run `estimate-cost`, show the USD cost, wait for explicit confirmation.
5. `start` to submit. Capture the ID.
6. Launch `download-results` through the current host's documented background or resumable command facility. Discover its arguments rather than assuming another host's session API. Preserve the returned process/job handle; `download-status` plus the run directory remain the durable source of truth. Use recurring monitoring only when that capability exists and the user has authorized it; otherwise report the exact status command. After launch, report the job ID, run name, output directory, and any actually configured next check.
7. Rank hits from `<output-root>/<run-name>/results/index.jsonl` by `binding_confidence` descending. Use `iptm` and `min_interaction_pae` as tiebreakers. `optimization_score` is not emitted for this endpoint. Read [references/results.md](references/results.md) for output layout and metric details.

## Command Pattern

```bash
# Replace placeholders with concrete absolute paths before running.
# Use a short descriptive run name, for example: protein-screen-<target>-<library>-v1

boltz-api protein:library-screen estimate-cost \
  --input @yaml:///absolute/path/payload.yaml

boltz-api protein:library-screen start \
       --idempotency-key "<run-name>" \
       --input @yaml:///absolute/path/payload.yaml \
       --raw-output --transform id

# Copy the printed job ID into this command, then launch it in the agent
# runtime's background/non-blocking mode.
# Use the current host's documented background/session facility and preserve its handle.
# Do not assume shell-backgrounded child processes survive tool completion.
boltz-api download-results \
  --id "<job-id-from-start>" --name "<run-name>" \
  --root-dir "/absolute/path/boltz-experiments" \
  --poll-interval-seconds 30
```

Payload keys are `proteins`, `target` — API body field names.

## Always Do This

- For `structure_template`, embed CIF/PDB bytes with `@data:///abs/path/target.cif` inside the `structure.data` field. Don't use bare `@path` (automatic file-type detection once sent CIF as plain text into a base64 field and broke the server parser).
- Residue indices are 0-based. `epitope_residues` and `flexible_residues` must be subsets of `crop_residues`.
- Keep payload field names exactly as the API body names shown in `references/api.md`.
- Use absolute paths for the output root, payload files, and embedded target files. Do not `cd` into the run directory for follow-up commands; pass the same `--root-dir` and use absolute paths so later relative paths do not drift.
- Prefer one merged top-level payload via `--input @yaml:///absolute/path/payload.yaml` or `@json:///absolute/path/payload.json` for `estimate-cost` and `start`. Keep `--idempotency-key` and `--workspace-id` top-level; if they also appear inside `--input`, the top-level flags win.
- Direct object flags still work as overrides, such as `--target @yaml:///absolute/path/target.yaml` or repeated `--protein @json:///absolute/path/protein-1.json` entries. Piped YAML / JSON on stdin also works, but it must use API body field names. Never use `@file://` or `@./`.
- Use the same slug as both `--idempotency-key` and `--name`.
- In permission-gated agents such as Claude Code, keep each Boltz call as a top-level command that starts with `boltz-api`. Prefer concrete arguments over `sh -c`, inline environment assignments, aliases, wrapper scripts, loops, or pipelines around the `boltz-api` invocation unless the user already allowed that exact command form. Use `--raw-output --transform id`, read the printed ID, then paste that literal ID into the next `download-results` command.
- Prefer the current host's supported background or resumable command facility. If no durable command mode exists, explain the limitation and provide the exact downloader command for an interactive terminal. Do not invent session handles or hide an unmanaged process.
- After the background/session starts, do not manually wait on it or run ad hoc polling loops. Wall-clock time scales roughly with the number of candidates in the library: under 100 often finishes in a few minutes, 100-1,000 may take several minutes to tens of minutes, and larger screens can take longer or hours depending on inputs and system load. Don't quote a fixed duration. `--poll-interval-seconds 30` is a reasonable downloader default. `download-results` emits JSONL progress on stderr by default; add `--progress-format text --verbose` only when you explicitly want human-readable logs.
- If recurring monitoring is available and authorized, configure it to run `boltz-api --format json download-status --name "<run-name>" --root-dir "/absolute/path/boltz-experiments"` and stop once terminal. Choose cadence by candidate count: under 100 -> every 1-2 minutes; 100-1,000 -> every 5 minutes; over 1,000 -> every 15 minutes. Notify only on material changes or terminal completion/failure. Use the discovered process-status operation for user-requested interactive checks; do not assume `write_stdin` or any other host API exists. Never run a manual poll loop in the current turn.
- If the current host has no heartbeat automation support, do not claim an automatic next check. Report the job ID, run name, output directory, and the command needed to check `download-status`.
- If detached download needs to be restarted, re-run `boltz-api download-results` with the same `--name "<run-name>"` and the same `--root-dir`.
- Cost is tiered by total complex length (target + candidate); the combined length sets the tier. Do not state or estimate a dollar figure yourself — to say anything about cost, run `estimate-cost` and quote only the number it returns.

## Escape Hatch

- Payload reference: <https://api.boltz.bio/docs/api/python/resources/protein/subresources/library_screen/methods/start>
- CLI flag names: `boltz-api protein:library-screen start --help`

Read [references/api.md](references/api.md) for the `proteins` list shape and both `target` variants (structure_template with `chain_selection`, and no_template with epitope hints). Read [references/results.md](references/results.md) after download when ranking screened binders or explaining outputs.

## Outputs

Rank from `results/index.jsonl` after `download-results`; use [references/results.md](references/results.md) for local file layout and metric meanings.