分子对接—蛋白和小分子对接结果自动可视化

# ============================================================
# step1_docking_visualization.pml
# AutoDock Vina docking visualization in PyMOL
#
# Input files:
#   D:/work/rep.pdbqt
#   D:/work/output.pdbqt
#
# Workflow:
#   1. Load receptor and docking result
#   2. Keep only MODEL 1 / best Vina pose
#   3. Create pro and lig objects
#   4. Save combined result.pdb
#   5. Show protein cartoon and ligand sticks
#   6. Detect polar contacts
#   7. Show interacting residues as sticks
#   8. Use a white background
#
# Note:
#   This version intentionally keeps PyMOL's default lighting,
#   shadows, depth cue and most rendering parameters, so that
#   the visual appearance remains close to normal manual operation.
# ============================================================

# ---------- 0. Start from a clean session ----------
reinitialize

# ---------- 1. Load receptor ----------
load D:/work/rep.pdbqt, pro

# ---------- 2. Load Vina docking output ----------
load D:/work/output.pdbqt, lig_all

# Keep only the first docking pose / MODEL 1
create lig, lig_all, 1, 1
delete lig_all

# ---------- 3. Save receptor + ligand ----------
save D:/work/result.pdb, pro or lig

# ---------- 4. Basic representations ----------
hide everything, all

show cartoon, pro
show sticks, lig

color lightblue, pro
color raspberry, lig

# ---------- 5. Detect ligand-protein polar contacts ----------
# mode=2 follows PyMOL's polar-contact style detection
distance lig_polar_contacts, lig, pro, mode=2

# Set hydrogen-bond / polar-contact color
set dash_color, lightorange, lig_polar_contacts

# Keep first figure clean: do not show distance labels yet
hide labels, lig_polar_contacts

# ---------- 6. Select protein residues involved in polar contacts ----------
select contact_res, byres ( \
    (pro and acceptor within 3.6 of (lig and donor)) or \
    (pro and donor within 3.6 of (lig and acceptor)) \
)

show sticks, contact_res
color lightorange, contact_res

# ---------- 7. Background ----------
bg_color white

# ---------- 8. Focus on binding pocket ----------
orient pro or lig
zoom lig or contact_res, 8

# ---------- 9. Summary ----------
print "============================================================"
print "Step 1 finished."
print "pro                 = receptor protein"
print "lig                 = Vina MODEL 1 / best pose"
print "contact_res         = protein residues involved in polar contacts"
print "lig_polar_contacts  = polar-contact distance object"
print ""
print "Combined structure saved to D:/work/result.pdb"
print ""
print "Now manually rotate/zoom and export Figure 1."
print "Then run:"
print "  @D:/work/step2_add_labels.pml"
print "============================================================"

# ============================================================
# step2_add_labels.pml
# Add hydrogen-bond distance labels and residue labels
#
# Prerequisite:
#   Run step1_docking_visualization.pml first
#   in the SAME PyMOL session.
#
# Label style:
#   Hydrogen-bond distance: 1 decimal place
#   Residue label: GLU166 format
#   Residue label larger than distance label
#   No bold font
# ============================================================

# ---------- 1. Show polar-contact distance labels ----------
show labels, lig_polar_contacts

# One decimal place, e.g. 2.8
set label_digits, 1, lig_polar_contacts

# Hydrogen-bond distance label appearance
set label_size, 16, lig_polar_contacts
set label_color, black, lig_polar_contacts
set label_font_id, 5, lig_polar_contacts

# ---------- 2. Label interacting residues ----------
# Label only CA atoms so each residue receives only one label.
# Example: GLU166, HIS163, ASN142
label contact_res and name CA, resn + resi

# Residue labels are intentionally larger than distance labels
set label_size, 22, contact_res
set label_color, black, contact_res
set label_font_id, 5, contact_res

# Small positional offset so labels do not sit directly on atoms
set label_position, (1.2, 1.2, 1.2), contact_res

# ---------- 3. Ensure intended representations remain visible ----------
show cartoon, pro
show sticks, lig
show sticks, contact_res
show dashes, lig_polar_contacts

bg_color white

# ---------- 4. Summary ----------
print "============================================================"
print "Step 2 finished."
print "Hydrogen-bond distances are shown with 1 decimal place."
print "Interacting residues are labeled as GLU166 / HIS163 / etc."
print "Residue labels are larger than distance labels."
print ""
print "Now manually rotate/zoom and export Figure 2."
print "============================================================"

@D:/work/step1_docking_visualization_v2.pml

@D:/work/step2_add_labels_v2.pml

#氢键
set label_size, 16, lig_polar_contacts
#氨基酸
set label_size, 20, lig_polar_contacts