R08.05.01.01 · 任务小类

分子可视化与配图

Molecular visualization & figures

Select, color and compose publication figures and measurements.

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: ChimeraX · PyMOL · VMD
小类 GUI 需求标签: HY · 混合

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。

R08.05.01.01-T01 Style HIV protease with cartoon, chain colours and a magenta ligand in ChimeraX

原始指令

Open input/1hsg.cif in ChimeraX. Show the protein as cartoon coloured by chain, the inhibitor MK1 as sticks coloured magenta, hide all waters and other atoms, and save the session as output/s1.cxs.

平台: mac · macOS win · Windows
应用: UCSF ChimeraX
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 2 / 5

建议验证方式

Grader reopens s1.cxs in headless ChimeraX and queries state: all protein residues ribbon-displayed, chains A/B in distinct colours, MK1 atoms displayed as sticks with colour (255,0,255), no water or other protein atoms displayed.

建议部分得分

30% cartoon; 20% chain colours; 35% ligand style and colour; 15% waters hidden.

R08.05.01.01-T02 Select residues within 5 Å of the ligand, show them as labelled sticks and save

原始指令

In ChimeraX open input/1hsg.cif, select all protein residues with any atom within 5 Å of MK1, show them as sticks with residue name/number labels, keep the rest as cartoon, and save output/pocket.cxs.

平台: mac · macOS win · Windows
应用: UCSF ChimeraX
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 3 / 5

建议验证方式

Session state: displayed side-chain residue set equals the gold 5 Å set across both chains exactly; residue labels exist for exactly those residues; MK1 shown.

建议部分得分

50% residue set exact (scaled by Jaccard); 30% labels; 20% session saved with correct styles.

R08.05.01.01-T03 Measure a zinc–cysteine sulfur distance in PyMOL and save it as an object

原始指令

Open input/zn_protease.pdb in PyMOL. Create a distance object named zn_sg between the Zn ion and the SG atom of Cys145 in chain A, write the distance in Å (2 decimals) to output/answer.txt and save output/zn.pse.

平台: mac · macOS win · Windows
应用: PyMOL
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: CL · CLI 足够
交互原语: click · 指向与点击 vis · 视觉判断
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 2 / 5

建议验证方式

answer.txt within 0.01 Å of the coordinate distance. zn.pse must contain a distance object named zn_sg between exactly those two atoms (chain A, not B).

建议部分得分

60% distance value; 40% named distance object between correct atoms.

R08.05.01.01-T04 Compose an unobstructed, centred view of an ATP pocket for a figure in ChimeraX

原始指令

Open input/kinase_atp.cif in ChimeraX. Show cartoon, pocket residues within 4 Å of ATP as sticks and ATP as ball-and-stick, turn on silhouettes, white background, and orient the view so ATP is centred and not hidden by protein. Save output/pocket.cxs and a 1200×900 output/pocket.png.

平台: mac · macOS win · Windows
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
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 4 / 5

建议验证方式

Image 1200×900, white background. From the session camera: ATP centroid projects within 10% of image centre; ray casting shows ≥90% of ATP atoms unoccluded by protein; silhouettes on; residue set equals gold 4 Å set. ChimeraX's Python shell, Python-script opening, --nogui/--script launch and REST remote control are disabled; the camera must come from the saved session.

建议部分得分

25% styles, residue set, background and silhouettes; 35% unobstructed view; 25% centred; 15% image size.

R08.05.01.01-T05 Render a hydrophobic-residue surface of lysozyme in PyMOL at print resolution

原始指令

Open input/lysozyme.pdb in PyMOL. Show the molecular surface, colour residues A, I, L, M, F, W, V orange and all others white, set a transparent background, and ray-trace a 2400×1800 PNG at 300 dpi to output/lyso.png. Save output/lyso.pse.

平台: mac · macOS win · Windows
应用: PyMOL
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 3 / 5

建议验证方式

lyso.pse: surface shown, per-residue colours match the class rule for all residues. PNG 2400×1800, dpi metadata 300, alpha channel with transparent background pixels; ray-traced (no aliasing pattern of OpenGL capture).

建议部分得分

40% residue colouring; 20% surface; 20% image size/dpi; 20% transparent ray-traced output.

R08.05.01.01-T06 Align an MD trajectory and compute backbone RMSD over time in VMD

原始指令

Load input/protein.psf and input/traj.dcd (500 frames) in VMD. With the RMSD Trajectory Tool, align all frames on backbone atoms of frame 0 and compute Cα RMSD to frame 0. Save per-frame values to output/rmsd.dat and the mean over the last 100 frames to output/answer.json.

平台: mac · macOS win · Windows
应用: VMD
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP07 · 仿真结果
条件: 未声明
提案难度: 3 / 5

建议验证方式

rmsd.dat: 500 values within 0.01 Å of reference (align on backbone, measure Cα); mean within 0.01 Å. Aligning and measuring on the same selection gives a measurably different series.

建议部分得分

30% alignment selection; 50% RMSD series; 20% mean value.

R08.05.01.01-T07 Superpose an AlphaFold model on a crystal structure and colour by deviation

原始指令

In ChimeraX open input/af_model.pdb and input/xtal.cif, superpose with matchmaker (Needleman–Wunsch, iterate at 2.0 Å), colour the model's residues by Cα distance to their matched residue on a 0–5 Å blue–red palette, label residues deviating >3 Å, save output/dev.cxs and list them in output/deviant.csv.

平台: mac · macOS win · Windows
应用: UCSF ChimeraX
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 3 / 5

建议验证方式

Matchmaker pruned RMSD within 0.01 Å of reference; deviant residue set exact; sampled residue colours consistent with the palette mapping (±10 RGB).

建议部分得分

30% superposition; 30% colour mapping; 40% deviant residue list.

R08.05.01.01-T08 Build three named figure scenes for a protein–ligand complex in PyMOL

原始指令

Open input/complex.pdb in PyMOL and create scenes 'overview' (whole protein cartoon in frame), 'pocket' (ligand-centred close-up with residues within 4 Å as sticks) and 'hbonds' (polar contacts between ligand and protein as dashes). Save output/figs.pse.

平台: mac · macOS win · Windows
应用: PyMOL
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: CL · CLI 足够
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 3 / 5

建议验证方式

figs.pse holds the three named scenes. overview: protein bounding box inside the view frustum; pocket: view centred within 2 Å of ligand centroid, zoom ≤25 Å; hbonds: distance object pairs equal the reference polar contacts.

建议部分得分

30% overview; 35% pocket view and residues; 35% polar contacts.

R08.05.01.01-T09 Set a cryo-EM map contour by model enclosure and colour the map zone by chain

原始指令

In ChimeraX open input/emd_map.mrc and input/model.cif. Set the map threshold so 95% of model heavy atoms lie inside the contour and record it, show the map within 3 Å of chain B as mesh, colour map zones by nearest chain, and save output/em.cxs and a 1600×1200 output/em.png.

平台: mac · macOS win · Windows
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: CL · CLI 足够
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 5 / 5

建议验证方式

Session threshold within 5% of the level enclosing 95% of heavy atoms; mesh style with zone radius 3 Å around chain B; colour-zone settings present; image 1600×1200 with mesh pixels present. ChimeraX's Python shell, Python-script opening, --nogui/--script launch and REST remote control are disabled; the threshold must be stored in the session.

建议部分得分

35% threshold; 25% chain-B zone; 25% colour by chain; 15% image.

R08.05.01.01-T10 List ligand–protein hydrogen bonds with VMD's HBonds representation

原始指令

Open input/complex.pdb in VMD. Add an HBonds representation between the ligand (resname LIG) and protein with donor–acceptor cutoff 3.2 Å and angle cutoff 20°. Write each donor–acceptor pair to output/hbonds.csv and save the visualization state to output/state.vmd.

平台: mac · macOS win · Windows
应用: VMD
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP02 · 记录 / 表格
条件: 未声明
提案难度: 3 / 5

建议验证方式

Pair set must equal the reference from VMD's measure hbonds with the same cutoffs in both directions; state.vmd must contain an HBonds rep with 3.2 / 20 parameters and the stated selection.

建议部分得分

60% pair set exact (scaled); 40% representation parameters.

R08.05.01.01-T11 Mutate a buried leucine to tryptophan choosing the least-clashing rotamer in PyMOL

原始指令

Open input/enzyme.pdb in PyMOL. With the Mutagenesis wizard mutate Leu88 of chain A to Trp, choose the rotamer with the fewest steric clashes shown by the wizard, apply it, and save output/L88W.pdb.

平台: mac · macOS win · Windows
应用: PyMOL
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: 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: 3 / 5

建议验证方式

A:88 must be TRP; χ1/χ2 within 15° of the gold lowest-strain rotamer; no heavy-atom contact <2.2 Å to other residues; all other atoms unchanged (RMSD 0).

建议部分得分

30% mutation applied; 50% correct rotamer; 20% no other changes.

R08.05.01.01-T12 Colour a structure by B-factor with a labelled colour key in ChimeraX

原始指令

In ChimeraX open input/structure.cif, colour atoms by B-factor with palette blue:white:red over 10–80 Å², add a colour key labelled 10, 45 and 80, and save output/bfac.cxs and a 1200×900 output/bfac.png.

平台: mac · macOS win · Windows
应用: UCSF ChimeraX
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 2 / 5

建议验证方式

50 sampled atoms must have colours matching the palette at their B-factor (±5 RGB); colour key model present with the three labels; PNG 1200×900.

建议部分得分

50% colour mapping; 30% colour key; 20% image.

R08.05.01.01-T13 Record a ligand-centred 360° rotation movie in ChimeraX

原始指令

In ChimeraX open input/complex.cif with the ligand shown as sticks. Set the centre of rotation to the ligand centroid and record a 6 s, 30 fps, 1280×720 H.264 movie rotating 360° about the vertical axis, saved as output/spin.mp4.

平台: mac · macOS win · Windows
应用: UCSF ChimeraX
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP05 · 时序媒体
条件: 未声明
提案难度: 4 / 5

建议验证方式

ffprobe: 180 frames, 1280×720, h264. First and last frames SSIM ≥0.98 (full turn); ligand pixel centroid (colour mask) stays within 20 px across frames, proving rotation about the ligand.

建议部分得分

25% format; 25% frame count; 30% rotation centred on ligand; 20% full 360°.

R08.05.01.01-T14 Assemble a three-panel structure figure from ChimeraX renders in Inkscape

原始指令

Make Figure 1 for input/complex.cif: A, cartoon coloured by domains in input/domains.csv; B, pocket close-up with labelled residues and H-bond pseudobonds; C, Coulombic surface (−10 to 10). Render each in ChimeraX (save sessions), lay them out in Inkscape at 180 mm width with bold panel letters, and export output/fig1.svg and a 600 dpi output/fig1.tif.

平台: mac · macOS win · Windows
应用: UCSF ChimeraX · Inkscape
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: CL · CLI 足够
交互原语: click · 指向与点击 drag · 拖放 vis · 视觉判断 multi · 跨应用
工作产物: WP03 · 视觉排版
条件: multiapp · 多应用 long · 长流程
提案难度: 5 / 5

建议验证方式

Three sessions verified (domain colours per CSV, pocket residues and H-bonds equal reference, Coulombic colouring range). fig1.svg: 3 images, text A/B/C bold, width 180 mm, no overlaps. TIFF 4252 px wide with 600 dpi tag. ChimeraX's Python shell, --nogui/--script and REST control are disabled, as is Inkscape's command-line export; a file-system audit flags figure files not written by Inkscape.

建议部分得分

20% panel A; 25% panel B; 20% panel C; 35% layout, letters and TIFF export.

R08.05.01.01-T15 Superimpose five kinases on their hinge residues in PyMOL and tabulate RMSD

原始指令

Load input/kin1.pdb to kin5.pdb in PyMOL. input/hinge.txt lists each structure's hinge residues (numbering differs). Superimpose all onto kin1 using Cα of those residues only, compute the 5×5 pairwise hinge Cα RMSD matrix, and save output/rmsd_matrix.csv and output/kinases.pse.

平台: mac · macOS win · Windows
应用: PyMOL
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单
工作产物: WP02 · 记录 / 表格
条件: 未声明
提案难度: 3 / 5

建议验证方式

Matrix symmetric with zero diagonal and values within 0.02 Å of reference pair_fit on the listed atoms; session objects superposed (kin2–5 hinge RMSD to kin1 matches matrix row 1).

建议部分得分

30% correct atom selections; 50% matrix values; 20% superposed session.

R08.05.01.01-T16 Render a GPCR-in-membrane system with selective lipid and ion display in VMD

原始指令

Load input/system.psf and system.pdb (GPCR in POPC with water and NaCl) in VMD. Show protein as NewCartoon coloured by secondary structure, lipid phosphorus atoms as tan VDW spheres, hide lipid tails and water, show only Na+ within 5 Å of protein, draw the periodic box, and render a 2000×1500 Tachyon image output/membrane.tga. Save output/state.vmd.

平台: mac · macOS win · Windows
应用: VMD
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 4 / 5

建议验证方式

state.vmd reps: NewCartoon/Structure on protein; VDW tan on 'lipid and name P'; Na+ selection within 5 of protein (atom count matches reference); no water/tail reps; pbc box drawn. Render 2000×1500 Tachyon output.

建议部分得分

20% protein rep; 25% lipid P spheres; 25% ion selection; 30% hidden components, box and render.

R08.05.01.01-T17 Control: list residues within 5 Å of the HIV protease ligand with a script

原始指令

Control pair of T02. Without a GUI, use Biopython or headless ChimeraX from the terminal to list all protein residues with any atom within 5 Å of MK1 in input/1hsg.cif and write them to output/residues.csv (chain, resname, resnum).

平台: mac · macOS lin · Linux
应用: Biopython · UCSF ChimeraX
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: WP02 · 记录 / 表格
条件: 未声明
提案难度: 2 / 5

建议验证方式

Residue set equal to the T02 gold set. Scored as the CLI control of T02.

建议部分得分

80% residue set (scaled by Jaccard); 20% CSV format.

R08.05.01.01-T18 Measure buried surface area of a protein–protein interface in ChimeraX

原始指令

Open input/complex_AB.cif in ChimeraX. Measure the buried surface area between chains A and B, colour interface residues of A orange and of B cyan, and write BSA (Å²) and the residue lists to output/interface.json. Save output/interface.cxs.

平台: mac · macOS win · Windows
应用: UCSF ChimeraX
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: CL · CLI 足够
交互原语: click · 指向与点击 type · 文字与表单 vis · 视觉判断
工作产物: WP12 · 答案 / 决策
条件: 未声明
提案难度: 3 / 5

建议验证方式

BSA within 2% of the reference measure buriedarea value; interface residue sets Jaccard ≥0.95 per chain; session colours match the lists.

建议部分得分

40% BSA; 40% residue sets; 20% colouring.

R08.05.01.01-T19 Find and colour the loop circled in a paper figure by matching the view in ChimeraX

原始指令

input/ref_view.png is a published figure of input/enzyme.cif with a loop circled that occludes the active-site entrance; no residue numbers are given. In ChimeraX reproduce the view, identify the loop residues, colour them red, save output/loop.cxs and list the residues in output/loop.txt.

平台: mac · macOS win · Windows
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
工作产物: WP10 · 标注
条件: 未声明
提案难度: 5 / 5

建议验证方式

Residue range Jaccard ≥0.8 with the gold loop; only those residues red in the session. Rendered session view vs ref_view.png SSIM is logged for partial credit. The figure has no metadata or caption naming residues. ChimeraX's Python shell, script opening and REST remote control are disabled.

建议部分得分

20% matching view (SSIM ≥0.6); 60% loop residues (scaled); 20% colouring.

R08.05.01.01-T20 Find the ligand exit frame in an unbinding trajectory and render consistent snapshots

原始指令

Load input/unbind.psf and input/unbind.dcd (2,000 frames) in VMD. Find the first frame where the ligand centre of mass is more than 10 Å from the pocket centre (residues in input/pocket.txt), then render frames 0, exit−50, exit and last with identical camera and styles to output/snap_*.png. Write the exit frame to output/answer.json.

平台: mac · macOS win · Windows
应用: VMD
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: CL · CLI 足够
交互原语: nav · 平移 / 缩放 / 滚动 click · 指向与点击 vis · 视觉判断 av · 音视频时序
工作产物: WP03 · 视觉排版
条件: 未声明
提案难度: 4 / 5

建议验证方式

Exit frame within ±2 of gold. Four PNGs with equal size; static protein core region SSIM ≥0.9 across snapshots (same camera); ligand position in each image consistent with the frame (projected centroid within 30 px).

建议部分得分

40% exit frame; 30% four correct frames rendered; 30% consistent camera and styles.

已有研究映射

以下沿用研究目录中的基准与小类映射，不是逐题标注、执行记录或产品背书。

分子可视化与配图

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已有研究映射

同工作流族的小类