R08.05.01.02 · 任务小类

密度图中建模

Model building into density maps

Build and refine atomic models into cryo-EM or X-ray maps.

20 条本项目编写的提案 · 分类 v1.1 · 新增基准运行 0 次。下方验证方式与部分得分规则是设计，不是执行结果。

典型应用: Coot · ChimeraX ISOLDE
小类 GUI 需求标签: G3 · 仅 GUI

任务提案 · 20

展开查看完整原文与建议检查方式；两种界面均保留提案英文原文。

R08.05.01.02-T01 Refit three side chains that sit out of density in Coot

原始指令

Open input/model.pdb and input/map.mtz (2.0 Å X-ray, 2mFo-DFc and mFo-DFc) in Coot. Side chains of A:Arg57, A:Glu102 and B:Lys33 lie outside density. Refit each into density (rotamer choice plus real-space refinement) without moving other residues, and save output/fixed.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

phenix.map_model_cc: RSCC ≥0.8 for each of the three residues; all other atoms RMSD <0.2 Å from input. Coot's Python/Scheme consoles and --script mode are disabled and PHENIX/CCP4 tools are absent; the session event log must show interactive refinement.

建议部分得分

90% residues with RSCC ≥0.8 (30 pts each); 10% rest of model unchanged.

R08.05.01.02-T02 Place ATP into difference density near His57 and refine it in Coot

原始指令

input/model.pdb and input/map.mtz show a strong positive mFo-DFc blob next to A:His57. Using the ATP dictionary input/ATP.cif, place ATP into that density in Coot, fit and real-space refine it, keep occupancy 1.0 and save output/with_atp.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断 geom · 精确几何
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 4 / 5

建议验证方式

Ligand heavy-atom RMSD to gold <1.0 Å (symmetry-aware); ligand RSCC ≥0.8; no ligand–protein contact <2.2 Å; protein unchanged (RMSD <0.2 Å). Automated ligand fitting programs (phenix.ligandfit) are absent. Coot's Python/Scheme consoles are disabled, and a file-system audit flags PDBs not written by Coot.

建议部分得分

20% ligand added with correct name and occupancy; 50% placement RMSD (full <1 Å, zero >3 Å); 20% RSCC; 10% no clashes.

R08.05.01.02-T03 Mutate a serine to alanine and real-space refine the residue in Coot

原始指令

Open input/model.pdb and input/map.mtz in Coot. Mutate A:Ser45 to Ala, real-space refine residues 44–46, and save output/S45A.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: click · 指向与点击 vis · 视觉判断
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 2 / 5

建议验证方式

A:45 must be ALA with CB present and no OG; residues 44–46 geometry within MolProbity norms (no new outliers); all other atoms unchanged (RMSD <0.05 Å). Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

60% correct mutation; 20% local refinement clean; 20% rest unchanged.

R08.05.01.02-T04 Fix two Ramachandran outliers while keeping the fit to density

原始指令

Validation of input/model.pdb against input/map.mtz flags Ramachandran outliers at A:77 and A:210. In Coot correct them (peptide flips, real-space refinement with restraints) so neither is an outlier, keep the backbone in density, and save output/rama_fixed.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

MolProbity: zero Ramachandran outliers; RSCC of residues 75–79 and 208–212 ≥ input values −0.02; atoms outside those windows RMSD <0.2 Å from input. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

80% outliers fixed (40 pts each); 20% fit and rest of model preserved.

R08.05.01.02-T05 Fit a displaced domain into a 3.2 Å cryo-EM map with ISOLDE

原始指令

In ChimeraX with ISOLDE, open input/model.cif and input/map.mrc (3.2 Å). Domain 2 (residues 220–380) is displaced ~4 Å and rotated ~8°. Use interactive MD, tugging and restraints to fit it, settle the model, and save output/fitted.cif.

平台: mac · macOS win · Windows lin · Linux
应用: UCSF ChimeraX · ISOLDE
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: drag · 拖放 rt · 实时控制 vis · 视觉判断 geom · 精确几何
工作产物: WP04 · 三维 / 空间模型
条件: long · 长流程
提案难度: 5 / 5

建议验证方式

phenix.validation_cryoem: CC_mask ≥0.75, clashscore <10, Ramachandran favored ≥95%, rotamer outliers <2%; domain-2 Cα RMSD to deposited model <1.5 Å. Rigid-body only fitting cannot reach the CC threshold; ChimeraX's Python shell and script opening are disabled and PHENIX command-line tools are absent from the agent VM.

建议部分得分

40% domain placement RMSD; 25% CC_mask; 20% geometry metrics; 15% no new chain breaks.

R08.05.01.02-T06 Add ordered waters and remove false waters from ligand density in Coot

原始指令

Open input/model.pdb and input/map.mtz in Coot. Add waters at peaks above 1.4 rmsd in 2mFo-DFc that make 2.4–3.2 Å contacts to H-bond partners, then delete any water placed inside the elongated density of the bound cryoprotectant near A:Tyr140. Save output/waters.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

≥85% of gold waters matched within 0.5 Å; false waters (no gold match) <10% of added; zero waters inside the cryoprotectant envelope; macromolecule unchanged. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

40% recall; 30% precision; 30% cryoprotectant density cleared.

R08.05.01.02-T07 Build a missing eight-residue loop into density in Coot

原始指令

input/model.pdb lacks residues A:145–152; their sequence is in input/seq.fasta and density is visible in input/map.mtz. Build the loop in Coot so it connects 144 and 153, fits the density, and has acceptable geometry. Save output/loop.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断 geom · 精确几何
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 4 / 5

建议验证方式

Residues 145–152 present with correct sequence; loop Cα RMSD to gold <1.5 Å; peptide bonds to 144/153 1.33±0.05 Å; ≥6 of 8 Ramachandran-favored; no clash <2.2 Å; loop RSCC ≥0.7. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

20% residues and sequence; 40% loop Cα RMSD; 20% geometry; 20% density fit.

R08.05.01.02-T08 Correct five rotamer outliers into density in Coot

原始指令

input/validation.txt lists five rotamer outliers in input/model.pdb. In Coot, for each, pick a rotamer that fits input/map.mtz density and refine. Do not alter other residues. Save output/rotamers_fixed.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 vis · 视觉判断
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

MolProbity rotalyze: none of the five is an outlier; each has RSCC ≥0.8 and χ angles within 20° of gold; other residues RMSD <0.1 Å. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

90% residues fixed and fitting (18 pts each); 10% rest unchanged.

R08.05.01.02-T09 Detect and correct a one-residue register shift in a helix

原始指令

In input/model.pdb the helix A:210–230 was built one residue out of register (sequence shifted by +1). Using side-chain density in input/map.mtz (aromatics and prolines) in Coot, confirm the shift, rebuild the helix with the correct sequence register from input/seq.fasta, refine, and save output/register_fixed.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 5 / 5

建议验证方式

For residues 210–230, each Cα within 1.0 Å of the gold Cα for the same residue identity (≥90% of residues); sequence matches seq.fasta; mean side-chain RSCC ≥0.75; flanking connections intact. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

25% shift direction identified; 45% residues in register (scaled); 20% side-chain fit; 10% connectivity.

R08.05.01.02-T10 Decide which flagged peptides need flipping and flip only those in Coot

原始指令

input/cablam.txt lists six backbone outliers in input/model.pdb. Inspect the carbonyl density in input/map.mtz in Coot: flip the peptide planes whose carbonyl oxygen points out of density, leave the others, refine locally and save output/flipped.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 vis · 视觉判断
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

For the three gold flips, carbonyl O within 0.5 Å of gold; the other three peptides unchanged (O moved <0.3 Å). Flipping all six fails half the positions. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

60% correct flips (20 pts each); 40% correctly untouched peptides (≈13 pts each).

R08.05.01.02-T11 Correct cis-peptide and chirality errors flagged by ISOLDE validation

原始指令

Open input/model.cif and input/map.mrc in ChimeraX with ISOLDE. ISOLDE's markup flags three non-proline cis peptides and one inverted Cα chirality. Correct them with ISOLDE's tools during a short simulation, settle, and save output/corrected.cif.

平台: mac · macOS win · Windows lin · Linux
应用: UCSF ChimeraX · ISOLDE
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 rt · 实时控制 vis · 视觉判断
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

Zero non-proline cis peptides and correct L-chirality at all Cα; the four sites keep RSCC ≥ input −0.03; residues >8 Å from the sites RMSD <0.3 Å. The ChimeraX Python shell is disabled, so edits must be made interactively.

建议部分得分

60% cis peptides fixed (20 pts each); 25% chirality fixed; 15% fit and rest preserved.

R08.05.01.02-T12 Remove an unsupported alternate conformer and reset occupancy in Coot

原始指令

In input/model.pdb residue A:Glu88 has alternate conformers A and B at 0.5/0.5 occupancy, but input/map.mtz density supports only one of them. In Coot inspect the density, delete the unsupported conformer, set the remaining one's occupancy to 1.0 and clear its altloc, then save output/single_conf.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 vis · 视觉判断
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 2 / 5

建议验证方式

A:88 has one conformer with occupancy 1.00 and blank altloc whose coordinates equal the density-supported input conformer (gold; nothing in the file says which); no other atoms changed. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

50% correct conformer kept; 20% occupancy 1.0; 20% altloc cleared; 10% rest unchanged.

R08.05.01.02-T13 Build an N-linked glycan stub on Asn234 into density in Coot

原始指令

Density in input/map.mrc (3.0 Å cryo-EM) extends from A:Asn234 of input/model.pdb. With Coot's glycan tools add NAG-NAG-BMA (β1-4 linkages) attached to ND2, fit each sugar to density and refine. Save output/glycan.pdb with proper LINK records.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 vis · 视觉判断 geom · 精确几何
工作产物: WP04 · 三维 / 空间模型
条件: tutorial · 阅读文档 / 教程
提案难度: 4 / 5

建议验证方式

LINK records ND2–C1 (NAG1), O4–C1 for NAG1→NAG2 and NAG2→BMA; Privateer: all rings 4C1 chair and correct anomers; per-sugar RSCC ≥0.7; sugar positions within 1.5 Å of gold. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

25% three sugars present; 25% linkages; 25% ring conformations; 25% fit/placement.

R08.05.01.02-T14 Rigid-fit two AlphaFold domains separately into a cryo-EM map in ChimeraX

原始指令

In ChimeraX open input/af_model.pdb and input/map.mrc. Split the model at the linker (residue 205), place each domain by hand near its density and optimize with fitmap separately, then combine into one model, and save output/docked.pdb with the original chain ID.

平台: mac · macOS win · Windows lin · Linux
应用: UCSF ChimeraX
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G2 · GUI 必要
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: drag · 拖放 click · 指向与点击 vis · 视觉判断 geom · 精确几何
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

Each domain's Cα RMSD to the deposited model <1.5 Å; per-domain map correlation ≥0.7; output is one chain with residues in order and linker bond present. The ChimeraX Python shell is disabled, so edits must be made interactively.

建议部分得分

35% domain 1 placed; 35% domain 2 placed; 20% correlation; 10% merged single chain.

R08.05.01.02-T15 Identify a zinc site from anomalous density and place the ion in Coot

原始指令

input/model.pdb was built with water HOH 501 at a tetrahedral site formed by four Cys. Using input/map.mtz and the anomalous difference map input/anom.mtz in Coot, confirm the metal, replace the water with Zn (occupancy 1.0), refine, and save output/zn.pdb. Leave other waters as water.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 vis · 视觉判断 nav · 平移 / 缩放 / 滚动
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

Exactly one ZN atom within 0.5 Å of gold with occupancy 1.0 and Zn–SG distances 2.2–2.5 Å; HOH 501 removed; no other waters converted (three decoy peaks are true waters). Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

50% Zn placed correctly; 20% coordination geometry; 30% no decoy waters converted.

R08.05.01.02-T16 Refine a cryo-EM model in the PHENIX GUI and fix remaining clashes in Coot

原始指令

In the PHENIX GUI run real_space_refine on input/model.pdb against input/map.mrc (resolution 3.1 Å) with secondary-structure restraints and NCS. Review the validation results, then fix the remaining worst clashes and any Ramachandran outlier in Coot. Save output/final.pdb.

平台: mac · macOS lin · Linux
应用: PHENIX · Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: HY · 混合
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 vis · 视觉判断 multi · 跨应用
工作产物: WP04 · 三维 / 空间模型
条件: multiapp · 多应用
提案难度: 4 / 5

建议验证方式

phenix.validation_cryoem of final.pdb: clashscore <5, Ramachandran outliers 0, CC_mask ≥ input value; PHENIX job directory shows real_space_refine with SS and NCS enabled.

建议部分得分

25% refinement run with stated options; 30% clashscore; 25% Rama outliers; 20% CC_mask maintained.

R08.05.01.02-T17 Model a dual side-chain conformation with density-based occupancies

原始指令

Density in input/map.mtz around A:Ser150 of input/model.pdb shows two rotamers. In Coot add an alternate conformation, fit conformer A and B into the two lobes, set occupancies to match density (they must sum to 1.0), and save output/altconf.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 3 / 5

建议验证方式

A:150 has altlocs A/B with χ1 each within 20° of a gold rotamer (both lobes covered), occupancies summing to 1.0 and within 0.1 of gold; backbone unchanged. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

30% alternate conformation added; 40% both rotamers correct; 20% occupancies; 10% backbone unchanged.

R08.05.01.02-T18 Trace a 40-residue helix-turn-helix de novo into unmodelled density

原始指令

input/map.mrc (3.0 Å) contains unmodelled density for residues 400–439 of the sequence in input/seq.fasta. In Coot build a Cα/backbone trace (helix placement, baton building), assign the sequence in the correct direction and register, refine, and append it as chain A residues 400–439 to output/traced.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断 geom · 精确几何
工作产物: WP04 · 三维 / 空间模型
条件: long · 长流程
提案难度: 5 / 5

建议验证方式

Cα RMSD to gold <1.5 Å over 400–439; ≥90% residues registered correctly (Cα within 1.5 Å of same-identity gold Cα); chain direction correct; Ramachandran favored ≥90%. ModelAngelo/Buccaneer are absent. Coot's Python/Scheme consoles are disabled.

建议部分得分

25% backbone trace placed; 15% correct direction; 40% sequence register; 20% geometry.

R08.05.01.02-T19 Control: make the S45A mutation and refine with PHENIX command-line tools

原始指令

Control pair of T03. Without Coot or any GUI, mutate A:Ser45 to Ala in input/model.pdb using gemmi or phenix.pdbtools, refine residues 44–46 against input/map.mtz with command-line PHENIX tools, and save output/S45A.pdb.

平台: mac · macOS lin · Linux
应用: PHENIX · gemmi
交互表面: term · 终端
GUI 需求 · 任务设定: CL · CLI 足够
GUI 需求 · 普通权限: CL · CLI 足够
交互原语: code · 代码与命令
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 2 / 5

建议验证方式

Same checker as T03 (A:45 ALA, local geometry clean, rest RMSD <0.05 Å). Scored as the CLI control of T03.

建议部分得分

60% mutation; 20% geometry; 20% rest unchanged.

R08.05.01.02-T20 Build a covalent inhibitor on the catalytic cysteine with a link restraint

原始指令

Density in input/map.mtz shows a covalent inhibitor bonded to A:Cys25 of input/model.pdb. Place the ligand from input/inhibitor.cif in Coot, create the SG–C covalent link with the provided link dictionary input/link.cif, refine the ligand and Cys25 together, and save output/covalent.pdb.

平台: mac · macOS win · Windows lin · Linux
应用: Coot
交互表面: desk · 桌面 GUI
GUI 需求 · 任务设定: G3 · 仅 GUI
GUI 需求 · 普通权限: G2 · GUI 必要
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断 geom · 精确几何
工作产物: WP04 · 三维 / 空间模型
条件: 未声明
提案难度: 4 / 5

建议验证方式

LINK record between A:Cys25 SG and the ligand's warhead carbon with distance 1.75–1.90 Å; ligand heavy-atom RMSD to gold <1.0 Å; ligand RSCC ≥0.8; no clash <2.2 Å. Coot's Python/Scheme consoles and --script mode are disabled, PHENIX/CCP4 command-line tools are absent from the agent VM, and a file-system audit flags PDBs not written by Coot.

建议部分得分

30% ligand placed (RMSD); 30% covalent link record and distance; 20% density fit; 20% clean geometry.

已有研究映射

当前映射未给此小类指定基准参考。

密度图中建模

任务提案 · 20

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已有研究映射

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