SUMMARY
The discussion focuses on the use of PyMol and VESTA for visualizing crystal and protein structures, specifically for determining the nearest and next nearest neighbors of an atom in a crystal. Users can utilize the "distance" command in PyMol to measure distances and the "around" command to identify neighboring atoms. The conversation highlights the challenges of using non-window versions of software, particularly in exiting the program. PyMol is confirmed as a standard tool for analyzing protein crystal structures.
PREREQUISITES
- Familiarity with PyMol 2.5 for molecular visualization
- Understanding of crystal structure concepts
- Knowledge of command-line interface operations
- Basic skills in measuring atomic distances in molecular models
NEXT STEPS
- Explore PyMol's "distance" command for measuring atomic distances
- Research the "around" command in PyMol for identifying neighboring atoms
- Investigate VESTA for additional visualization capabilities of crystal structures
- Learn about command-line interface navigation to improve usability of non-window software
USEFUL FOR
This discussion is beneficial for chemists, crystallographers, and molecular biologists who require tools for visualizing and analyzing atomic structures in crystals and proteins.