1bqt_pymol_commands.pml

# ============================================================
# PyMOL Commands for 1bqt
# ============================================================
# Copy and paste these commands into PyMOL
# ============================================================

# Load structure (adjust path as needed)
load 1bqt.pdb

# Basic setup
hide all
show cartoon
color grey80, all

# Select and highlight critical residues (Top 10)
select critical_top10, resi 31+23+2+8+20+49+25+3+33+29 and chain A
show sticks, critical_top10
color red, critical_top10
set stick_radius, 0.3, critical_top10

# Label critical residues
label critical_top10 and name CA, "%s%s" % (resn,resi)
set label_size, 14
set label_color, red

# Create gradient coloring by importance (Top 5 in different reds)
select critical_rank1, resi 31 and chain A
color red, critical_rank1
select critical_rank2, resi 23 and chain A
color tv_red, critical_rank2
select critical_rank3, resi 2 and chain A
color salmon, critical_rank3
select critical_rank4, resi 8 and chain A
color lightsalmon, critical_rank4
select critical_rank5, resi 20 and chain A
color warmpink, critical_rank5

# Show surface around critical residues
show surface, byres (critical_top10 around 5)
set surface_color, white
set transparency, 0.5

# Center view on critical residues
zoom critical_top10

# ============================================================
# Additional useful commands:
# ============================================================
# To save session: save 1bqt_critical.pse
# To save image: png 1bqt_critical.png, dpi=300
# To highlight most critical (rank 1): select most_critical, critical_rank1
# ============================================================