Pymol_Scripts_Commands

List of Pymol commands frequently used:

1. RMSD Calculation: a. heavy atom:

   align mobile & not name H* , target & not name H* , cycles=100, transform=1
   

   b. Backbone

   align mobile & name P+OP1+OP2+O5'+O3'+C1'+C2'+C3'+C4'+O4' , target & name P+OP1+OP2+O5'+O3'+C1'+C2'+C3'+C4'+O4' , cycles=100, transform=1
   

2. Post docking see interactions between ligand and receptor

   # Select residues within 4 Å of ligand
   select near_residues, (byres (organic around 4))
   
   # Show only ligand-residue interactions (no internal ones)
   dist interactions, organic, near_residues, mode=2
   

3. Label residues at C1' atoms with resn-resi format

   label name C1', "%s-%s" % (resn, resi)