Molecular visualization & figures
Select, color and compose publication figures and measurements.
20 project-authored proposals · taxonomy v1.1 · 0 new benchmark runs. Verifiers and partial-credit rules below are designs, not executed results.
- Typical applications
- ChimeraX · PyMOL · VMD
- Class GUI-need label
HY· Hybrid
Task proposals · 20
Expand to inspect the complete original wording and proposed checks. Original proposal text remains English in both interfaces.
R08.05.01.01-T01 Style HIV protease with cartoon, chain colours and a magenta ligand in ChimeraX
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- PyMOL
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
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).
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
drag· Drag & dropclick· Point & clickvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- PyMOL
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
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).
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- VMD
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP07· Simulation result- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
Matchmaker pruned RMSD within 0.01 Å of reference; deviant residue set exact; sampled residue colours consistent with the palette mapping (±10 RGB).
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- PyMOL
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 5 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- VMD
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- PyMOL
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickvis· Visual judgment- Work product
WP04· 3D/spatial model- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
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).
Proposed partial credit
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
Original instruction
In ChimeraX open input/structure.cif, colour atoms by B-factor with palette blue:white:red over 10–80 Ų, add a colour key labelled 10, 45 and 80, and save output/bfac.cxs and a 1200×900 output/bfac.png.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
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.
Proposed partial credit
50% colour mapping; 30% colour key; 20% image.
R08.05.01.01-T13 Record a ligand-centred 360° rotation movie in ChimeraX
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP05· Time-based media- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX · Inkscape
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clickdrag· Drag & dropvis· Visual judgmentmulti· Cross-app- Work product
WP03· Visual layout- Conditions
multiapp· Multi-applong· Long-horizon- Proposed difficulty
- 5 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- PyMOL
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & forms- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
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).
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- VMD
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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).
- Platforms
mac· macOSlin· Linux- Applications
- Biopython · UCSF ChimeraX
- Interfaces
term· Terminal- GUI need · task setting
CL· CLI-sufficient- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
code· Code & commands- Work product
WP02· Records/table- Conditions
- None declared
- Proposed difficulty
- 2 / 5
Proposed verifier
Residue set equal to the T02 gold set. Scored as the CLI control of T02.
Proposed partial credit
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
Original instruction
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 (Ų) and the residue lists to output/interface.json. Save output/interface.cxs.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
click· Point & clicktype· Text & formsvis· Visual judgment- Work product
WP12· Answer/decision- Conditions
- None declared
- Proposed difficulty
- 3 / 5
Proposed verifier
BSA within 2% of the reference measure buriedarea value; interface residue sets Jaccard ≥0.95 per chain; session colours match the lists.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- UCSF ChimeraX
- Interfaces
desk· Desktop GUI- GUI need · task setting
G2· GUI-essential- GUI need · ordinary access
G2· GUI-essential- Interaction primitives
drag· Drag & dropclick· Point & clickvis· Visual judgment- Work product
WP10· Annotations- Conditions
- None declared
- Proposed difficulty
- 5 / 5
Proposed verifier
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.
Proposed partial credit
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
Original instruction
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.
- Platforms
mac· macOSwin· Windows- Applications
- VMD
- Interfaces
desk· Desktop GUI- GUI need · task setting
HY· Hybrid- GUI need · ordinary access
CL· CLI-sufficient- Interaction primitives
nav· Pan/zoom/scrollclick· Point & clickvis· Visual judgmentav· Audio/video over time- Work product
WP03· Visual layout- Conditions
- None declared
- Proposed difficulty
- 4 / 5
Proposed verifier
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).
Proposed partial credit
40% exit frame; 30% four correct frames rendered; 30% consistent camera and styles.
Mapped research references
Existing benchmark-to-class links from the research catalog. They are not record-level annotations, executions or product endorsements.