How to show distance between residues in Pymol

Question

With the this PDB file and the following PyMOL code:

cd /Users/foo/Desktop/
reinitialize
load pdp_4gg6CD1_I.pdb
as cartoon 
select chainI, chain I
select chainC, chain C 
select chainD, chain D 
show sticks, chainI
spectrum count, cyan_red, chainI
color yellow, chain C

I can make this image:

What I want to do is to show the distance between the selected residues in chainC (yellow) with chainI (stick).

The selected residues of chainC that I want is this:

[9, 23, 25, 44, 53, 54, 55, 59, 62, 63, 66]

Y    Y   H   W  R   R   F    F   T  N    V

How can I do that?

Do you want to get the closest distance between one atom in your selection from chain C and another atom from chain I? Getting the distance of all atoms your selection to all atoms in chain I is easier but but the answer is quite messy. — Maximilian Peters, Jun 25 '16 at 17:27

score 3 · Accepted Answer · answered Jun 29 '16 at 22:14

Let's use cmd.iterate to get all the atoms in a selection (chain C and chain I) and write the coordinates and atom name to dictionaries for later use.
Then we can calculate all the distances between all atoms and write the closest residues and atom names to two lists (min_c and min_i)
In the last step we only have to draw the distance objects between the closest atoms and we are done :)

from math import sqrt

def closestAtoms(list1=[9, 23, 25, 44, 53, 54, 55, 59, 62, 63, 66], list2=[5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17]):
    atoms = {}
    atoms2 = {}

    for r in list1:
        command = "chain C and resi %s" % (r)
        coordinates = {'atoms': []}
        cmd.iterate_state(-1, command, 'atoms.append([x, y, z, name])', space=coordinates)
        atoms[r] = coordinates['atoms']

    for i in list2:
        command = "chain I and resi %s" % (i)
        coordinates = {'atoms': []}
        cmd.iterate_state(-1, command, 'atoms.append([x, y, z, name])', space=coordinates)
        atoms2[i] = coordinates['atoms']

    for i in list2:
        min_dist = 10**3
        for c in list1:
            for cc in atoms[c]:
                for ii in atoms2[i]:
                    dist = sqrt((cc[0] - ii[0])**2 + (cc[1] - ii[1])**2 + (cc[2] - ii[2])**2)
                    if dist < min_dist:
                        min_dist = dist
                        min_c = [c, cc[3]]
                        min_i = [i, ii[3]]
        cmd.distance('dist_%s_%s' % (min_c[0], min_i[0]), 'chain C and resi %s and name %s' % (min_c[0], min_c[1]), 'chain I and resi %s and name %s' % (min_i[0], min_i[1]))

cmd.extend("closestAtoms", closestAtoms)

How to show distance between residues in Pymol

1 Answers1