Troubleshooting Common Issues in XtalDraw: Solutions & Best PracticesXtalDraw is a specialized molecular-graphics and model-building program widely used in macromolecular crystallography for building, editing, and visualizing atomic models within electron density maps. Like any specialized software, users can encounter recurring problems that slow progress or lead to incorrect models. This article collects common issues users face with XtalDraw, practical solutions, and best practices to avoid problems before they arise.
1. Installation and startup problems
Common symptoms
- XtalDraw fails to start or crashes on launch.
- Missing or incompatible libraries produce error messages.
- GUI appears distorted or unresponsive.
Solutions
- Verify system requirements: ensure your OS version and hardware meet XtalDraw’s requirements.
- Install required dependencies: check for required X11 or GUI libraries (on Linux), correct versions of Tcl/Tk if applicable, and any platform-specific libraries. Use your package manager or the binary distribution recommended by the developers.
- Run from a terminal to capture error output: start XtalDraw from the command line and record messages — they often point to missing libraries or permission problems.
- Check graphics drivers: update GPU drivers on Windows/Linux and ensure proper OpenGL support.
- Reinstall or use a clean environment: if issues persist, remove config files and reinstall; consider running in a container (Docker) or virtual environment to isolate conflicts.
Best practices
- Keep a snapshot of working binaries and note exact dependency versions.
- Use platform-provided packages if available (less likely to miss dependencies).
- For production systems, use containerized builds to ensure reproducibility.
2. File format and I/O errors
Common symptoms
- XtalDraw cannot open PDB, mmCIF, map (CCP4/MRC), MTZ, or map-like files.
- Unrecognized file format errors or silent failures when loading large files.
- Incorrect interpretation of column labels in MTZ files (e.g., amplitude vs. intensity, Rfree flags).
Solutions
- Validate file formats externally: use pdb-tools, phenix.pdbtools, cctbx, or CCP4 utilities to check file integrity and format compliance.
- Convert formats when necessary: use phenix.mtz2map, cctbx tools, or CCP4 programs to rebuild MTZ/map files correctly. Ensure map files have correct headers and byte-order for your platform.
- Check MTZ labels and content: ensure columns for F/FP/I and SIGF are properly named and that an Rfree column with correct flags exists. If XtalDraw expects certain labels, rename columns with MTZUTILS or phenix.reflection_file_editor.
- For very large maps, increase memory limits or split maps if supported; ensure XtalDraw is compiled/linked for 64-bit if using large datasets.
Best practices
- Keep canonical copies of original experimental files.
- Maintain a small validation script to check MTZ/mrc/pdb/mmCIF before loading into modeling tools.
- When exchanging files between programs, prefer mmCIF for coordinates and MTZ for reflections when supported.
3. Map display and density visualization issues
Common symptoms
- Electron density appears very noisy or too weak/strong at default contour levels.
- Map layers aren’t aligned with the model (off by origin or shifted).
- Contour controls seem unresponsive or map rendering is slow.
Solutions
- Adjust contour levels: try a range of sigma levels (e.g., 0.8–3.0) and inspect both 2Fo–Fc and Fo–Fc maps. Use RMS-based rather than absolute contouring if supported.
- Recalculate and check map coefficients: ensure map phases and coefficients are calculated correctly (2Fo–Fc uses appropriate combination of Fobs and Fc). Re-generate maps externally (Phenix/CCP4) to verify.
- Fix origin shifts: if map and model are misaligned, check map header ORIGIN and the model’s coordinates. Use tools (e.g., phenix.maps, CCP4’s mapmask or maprot) to re-center or apply origin shifts so both align. Ensure consistent use of fractional/Cartesian coordinates.
- Improve rendering performance: reduce map grid density or use lower-resolution subsets for interactive work; update graphics drivers; enable hardware acceleration if available.
Best practices
- Always verify map/model alignment immediately after loading — inspect a few clearly identifiable atoms/residues.
- Keep copies of maps at different contouring strategies to compare features.
- Use difference maps (Fo–Fc) to identify modeling errors, and always check hand-built changes against map changes.
4. Model-building and editing errors
Common symptoms
- Atoms move unexpectedly or commands produce no visible change.
- Broken geometry: distorted bond lengths/angles after automated operations.
- Tools for adding ligands, waters, or alternative conformations don’t behave as expected.
Solutions
- Check selection and active mode: ensure the correct chain/residue/atom is selected and the proper editing mode (move, twist, rotate, add) is active. Small UI inconsistencies can cause actions to apply to unintended objects.
- Use geometry restraints and refinement after edits: after manual moves, perform local real-space or reciprocal-space refinement to restore bond geometry (use external refinement tools if XtalDraw lacks robust restraints).
- Add ligands/waters carefully: ensure the ligand PDB/mmCIF has correct connectivity and that waters are added based on positive Fo–Fc peaks and hydrogen-bonding environment. Use external ligand-parameterization tools (e.g., eLBOW, Grade) when needed.
- Handle alternate conformations properly: create alternate location identifiers and set occupancy appropriately; adjust B-factors if occupancy changes. Confirm occupancy refinements using external refinement packages.
Best practices
- Make incremental edits and save versions frequently. Use clear file naming (model_v01.pdb, model_v02_after_loopbuild.pdb).
- Validate geometry with MolProbity or similar after substantial edits.
- Keep heavy manipulation tasks (ligand restraints, occupancy refinement) coupled with full refinement cycles in dedicated refinement software.
5. Refinement and validation mismatches
Common symptoms
- R/Rfree doesn’t improve after edits or becomes worse.
- Geometry validation shows many clashes or Ramachandran outliers despite reasonable map fit.
- Overfitting: good-looking maps but poor Rfree gap.
Solutions
- Perform proper refinement cycles: alternate rounds of manual building in XtalDraw with restrained reciprocal-space refinement (REFMAC, phenix.refine) rather than relying solely on real-space adjustments.
- Monitor Rfree and use cross-validation: ensure Rfree flags are preserved correctly through file edits and map generation. Recalculate Rfree sets if necessary.
- Balance geometry vs. fit: use weight optimization in refinement to avoid geometry degradation while improving fit; many refiners can optimize geometry restraints weight automatically.
- Use validation tools comprehensively: MolProbity, phenix.model_vs_data, and the PDB validation pipeline report can highlight issues not obvious in XtalDraw.
Best practices
- Keep an audit trail: document the changes, refinement parameters, and software versions used.
- Use conservative model adjustments when map quality is marginal.
- Always cross-check manually-built features with independent evidence (e.g., omit maps, biochemical data).
6. Scripting, macros, and automation problems
Common symptoms
- Custom scripts or macros fail or produce unexpected results.
- Batch operations work on some files but fail on others.
Solutions
- Check scripting API compatibility: ensure scripts match the XtalDraw version and its supported command set. Review logs for API deprecation warnings.
- Add robust error handling and input validation in scripts: check file existence, expected labels, chain IDs, and map headers before processing.
- Test scripts on minimal example datasets to ensure deterministic behavior before running on large batches.
- Use standard formats and canonical naming in scripts to minimize special-case handling.
Best practices
- Maintain version-controlled script repositories and include README with dependencies.
- Write unit tests for critical automation steps and integrate basic logging.
7. Crashes, stalls, and performance degradation
Common symptoms
- XtalDraw becomes unresponsive during large operations or after extended use.
- Sudden crash with no informative error dialog.
Solutions
- Inspect logs and run from terminal to capture stack traces or Python/Tcl errors.
- Increase system resources: close other memory-heavy applications, increase swap, or use a machine with more RAM/CPU/GPU power.
- Update to a newer stable XtalDraw build that includes performance fixes.
- Run memory-check tools (valgrind, address sanitizer builds) if compiling from source to catch leaks.
Best practices
- Save work frequently and keep incremental backups.
- For long tasks, consider running heavier computations (map calculation, large refinements) with command-line tools or clusters rather than interactive GUI.
8. Interoperability with other crystallography tools
Common symptoms
- Models or maps exported from XtalDraw appear incorrect in Coot, PyMOL, or refinement programs.
- Annotation, chain IDs, or altlocs get lost when transferring files.
Solutions
- Standardize on formats: prefer mmCIF for coordinates and MTZ for reflection data when exchanging between modern tools.
- Inspect header fields and ensure consistent use of chain IDs, residue numbering, and occupancy/altloc conventions. Use tools like pdb_fix or phenix.pdbtools to normalize files.
- When exporting maps, verify byte-order and header fields match the target program’s expectations.
Best practices
- Run a quick round-trip test: open exported files in the target program to detect issues early.
- Maintain simple, documented conventions for naming and numbering across collaborators.
9. Licensing and compatibility questions
Common symptoms
- Features unavailable due to licensing or build choices.
- Confusing differences between releases (e.g., feature present on one platform but not another).
Solutions
- Consult XtalDraw release notes and licensing documentation to determine feature availability.
- Use distributions or builds recommended by the developers for full feature access. If using a third-party build, confirm which optional features were compiled in.
Best practices
- Track the exact build/version of XtalDraw used for any publication or shared dataset.
- Prefer official releases for reproducibility.
10. User training and community support
Common symptoms
- Difficulty achieving expected modeling quality due to lack of familiarity.
- Uncertainty about best practices or workflow order.
Solutions
- Consult official documentation, tutorials, and example datasets provided by XtalDraw authors.
- Learn workflows from related tools (Coot, Phenix, CCP4) because many concepts are shared (map types, refinement cycles, validation).
- Ask specific questions on community forums or mailing lists; include minimal reproducible examples (input files, exact commands, and error messages).
Best practices
- Practice on well-characterized test datasets (e.g., benchmark structures) before editing critical experimental models.
- Keep a personal checklist for common tasks: map generation, alignment verification, geometry check, refinement step.
Conclusion
Most problems in XtalDraw stem from file-format mismatches, map/model alignment, insufficient refinement after edits, or platform-specific dependency issues. Quick wins include validating input files, checking origin alignment, using external refinement for geometry recovery, and preserving Rfree flags. For reproducibility and fewer surprises, adopt versioned files, containerized environments when possible, and an iterative build/refine/validate loop that combines XtalDraw’s interactive strengths with dedicated refinement and validation tools.