I can’t find recent web docs for XtalDraw right now, so I’ll give a practical troubleshooting guide based on common crystallographic model-building tools and likely XtalDraw behavior.
Troubleshooting Common XtalDraw Errors and Fixes
1) Program fails to start / crashes on launch
- Cause: Missing libraries or incompatible Python/Qt versions.
- Fix: Install required dependencies (matching Python, Qt/PyQt versions used by XtalDraw). Run from a terminal to capture error trace and install missing packages (e.g., PyQt5, NumPy). Try running with a clean user config (move ~/.xtaldraw or similar).
2) No electron density shown / map appears empty
- Cause: Map file format mismatch, wrong map coefficients, wrong map sigma scale or contour level.
- Fix: Confirm map file is a valid CCP4/MRC or MTZ map and that map coefficients were converted correctly. Recalculate map with appropriate phases/Fo/Fc and use sensible contour (e.g., 1.0–1.5σ). Try different contour levels and verify map origin and cell match your model.
3) Model and map misaligned
- Cause: Different origins or unit cell settings between model and map, or map uses fractional/Cartesian mismatch.
- Fix: Check model and map unit cell and symmetry; apply origin shifts or reindex/reorigin map to match the PDB coordinates. Use tools to compute and apply translation (or load both into a program that shows axes to compare).
4) Unable to load PDB / coordinate file
- Cause: Nonstandard formatting, very large files, or unsupported header records.
- Fix: Clean the PDB: remove nonstandard REM
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