Uploaded July 2019 | Updated September 2026, 8 hours ago
The default setting for PyMOL labels isn't great. Learn to resize and reposition labels with Dr. KP in this easy tutorial, and be on your way to making publication-quality images!
The default setting for PyMOL labels isn't great. Learn to resize and reposition labels with Dr. KP in this easy tutorial, and be on your way to making publication-quality images!



![PyMOL 101, Lesson 3: File Types and Saving – Publication Quality Figures & Scenes
In this lesson, KP takes you through the input and output PyMOL files, how to save your session, how to export a high-quality PNG image. Finally, we’ll learn to save scenes, preserving the different renderings and views as you work through this tutorial.
00:00 Intro
00:21 PDB and CIF files
01:41 Publication quality image guidelines and saving
04:41 Saving scenes in a PyMOL session
REFERENCES
• Rachel Kramer Green, Beginner’s Guide to PDB Structures and the PDBx/mmCIF Format https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/beginner%E2%80%99s-guide-to-pdb-structures-and-the-pdbx-mmcif-format
• PDB ID: 3uyn
• Elder, I., Fisher, Z., Laipis, P. J., Tu, C., McKenna, R., & Silverman, D. N. (2007). Structural and kinetic analysis of proton shuttle residues in the active site of human carbonic anhydrase III. PROTEINS: Structure, Function, and Bioinformatics, 68(1), 337-343.
***COMMAND LINE CODE to recreate the Lesson 2 structure***
fetch 3UYN, type=pdb1, multiplex=1
select zn, resn zinc
sele active, resi 5+7+62+64+67+94+96+119+199+200]
show sticks, active
zoom active
select active_water, ((resi 5+7+62+64+67+94+96+119+199+200, resn Zn)around 3.3) and(resn HOH)
hide nonbonded
show spheres, active_water
alter active_water, vdw=0.5
rebuild
hide sticks, name c+o+n PyMOL 101, Lesson 3: File Types and Saving – Publication Quality Figures & Scenes](https://i.ytimg.com/vi/ymkw7UMUnBw/mqdefault.jpg)

