by:view

/view — View Protein Structure

Open a protein structure in ProteinView in a tmux split pane with FullHD rendering.

Instructions

Step 1: Resolve the input

The argument can be:

• PDB ID (4 chars, e.g., 3DPL) — fetch from RCSB
• File path (e.g., .by/campaigns/.../design_003.cif) — open directly
• Design name (e.g., design_003) — search active campaign for matching CIF/PDB file

If a design name is given, find the file:

CAMPAIGN_DIR=$(cat .by/active_campaign 2>/dev/null)
FILE=$(find "$CAMPAIGN_DIR" -name "*${DESIGN_NAME}*.cif" -o -name "*${DESIGN_NAME}*.pdb" 2>/dev/null | head -1)

Step 2: Determine color scheme

Pick color based on context:

• If viewing a design with confidence data → --color plddt
• If viewing a multi-chain complex → --color chain
• If viewing a target structure → --color structure
• Default → --color chain

Step 3: Open in tmux split

tmux split-window -h "proteinview '${FILE_OR_PDB}' --fullhd --color ${COLOR}; read -p 'Press Enter to close'"

If the input is a PDB ID (no file):

tmux split-window -h "proteinview --fetch ${PDB_ID} --fullhd --color ${COLOR}; read -p 'Press Enter to close'"

Step 4: Confirm to user

━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 BY ► VIEWING: {name}
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━

Opened in tmux split pane (FullHD mode).
Color: {color scheme}
File: {path or PDB ID}

Controls: arrow keys to rotate, +/- to zoom, q to quit

Prerequisites

Check before running:

which proteinview >/dev/null 2>&1 || echo "NOT_INSTALLED"
echo "$TMUX" | grep -q "/" && echo "IN_TMUX" || echo "NOT_TMUX"

• If proteinview not installed: tell the user it's a separate tool and how to get it:

  ProteinView is not installed. It's a separate terminal protein viewer.
  Install: cargo install proteinview
  GitHub: https://github.com/001TMF/proteinview
  

  Then stop. Do not proceed.

• If not in tmux: tell the user this is a tmux feature:

  /by:view requires tmux (uses split panes for the viewer).
  Start tmux first: tmux new -s by
  

  Then stop. Do not proceed.