# assign the color into an object color red, Mos99 # assign the color into selected molecules select part1, Mos99 and chain A and resi 50+56+60 color hotpink, part1
Example of set a color by RGB value and assign it into an object
Create a variate ass which contain all ASP and GLU residues.
Distance
In pymol, you cannot calculate the distance between 2 residues. You can only do it on molecules. For calculate the distance between 2 residues, we could use alpha carbon (CA) as the reference
distance my_distance, 1tzg and chain P and resi 4 and name CA, 1tzg_H_L_P and chain H and resi 50 and name CA
For searching the nearest distance between 2 residues, a easiest way is using python pymol module.
But when if you could use python, than, maybe Biopython could be a better choice.
from pymol import cmd
# Load the structures (skip if already loaded) cmd.load("1tzg.pdb") cmd.load("1tzg_H_L_P.pdb")
# Select atoms in the specified residues residue1 = "1tzg and chain P and resi 4" residue2 = "1tzg_H_L_P and chain H and resi 50"
# Get atom identifiers for both residues atoms1 = cmd.get_model(residue1).atom atoms2 = cmd.get_model(residue2).atom
# Iterate over all atom pairs and calculate distances MIN = 1000 for atom1 in atoms1: for atom2 in atoms2: distance = cmd.get_distance(f"{residue1} and name {atom1.name}", f"{residue2} and name {atom2.name}") print(f"Distance between {atom1.name} in residue {atom1.resi} and {atom2.name} in residue {atom2.resi}: {distance:.2f} Å") if distance <= MIN: MIN = distance
Zoom
In pymol, you could zoom into a specific residues. Those different codes works differently. But they could achieve similar effects.
zoom 1tzg and chain A and resi 51 center 1tzg and chain A and resi 51 orient 1tzg and chain A and resi 51
Location Moving
Transition
# Moving the entire chain A 10 unit from 8a95 cmd.translate([10.0, 0.0, 0.0], '8a95 and chain A') cmd.rotate('z', 45, chain_to_move)