In this tutorial we will generate images showing the interaction of a ligand with its receptor. We aim to show the ligand, the residues in the ligand environment, hydrogen bonding interactions and the fold as transparent cartoon.
(1) Add low-energy hydrogen positions to the structure using the ProteinsPlus webserver.
(2) Use the following procedures to show hydrogen bonds within a ligand and its environment. Adopt the text written in italics to your complex structure. For the start you only need to change lines 2 and 3, the rest should work if only one ligand is bound to chain A, If not, use the resid selection to select only the ligand in the orthosteric binding pocket.
| (A) Show H bonds without hydrogens |
(B) Show H bonds with hydrogens |
| reinitialize load 4eiy_protoss.pdb select ligand, chain A and resn ZMA hide all select env, byres (ligand around 5.0) and not ligand show sticks, ligand or env show nb_spheres, env set h_bond_max_angle, 40 set h_bond_from_proton, 0 dist hbonds, ligand or env, ligand or env, mode=2 remove hydrogens hide labels, hbonds set dash_gap, 0.4 set dash_radius, 0.05 set dash_length, 0.3 hide labels, hbonds color grey50, hbonds color gold, ele C and ligand color grey70, ele C and env show cartoon, chain A set cartoon_color, grey70 set cartoon_transparency, 0.8 bg white orient ligand |
reinitialize load 4eiy_protoss.pdb select ligand, chain A and resn ZMA hide all select env, byres (ligand around 5.0) and not resn ligand show sticks, ligand or env set h_bond_max_angle, 40 set h_bond_from_proton, 1 dist hbonds, ligand or env, ligand or env, mode=2 hide labels, hbonds set dash_gap, 0.4 set dash_radius, 0.05 set dash_length, 0.3 hide labels, hbonds color grey50, hbonds color gold, ele C and ligand color grey70, ele C and env show cartoon, chain A set cartoon_color, grey70 set cartoon_transparency, 0.8 bg white orient ligand |
Copy-paste the procedure to a new pml script file that you generate in a text editor: my_image.pml
Orient the structure with the mouse to find a view that shows the most important interactions of the ligand. Adjust the clip and translate the view along the z-axis using ctrl-mouse-wheel to get a good view. If necessary, omit "unimportant" residues that are in front of the ligand.
Replace the selection command for env in your script with the following three lines. Show only side chains for residues that interact with their side chains only and specify them in the first line.
select omit_resids, chain A and resid 1000+2000
select mc_resids, chain A and resid 1001+2001
select env, (((byres (ligand around 5.0) and not ligand) and not
(polymer and name C+N+O)) or mc_resids) and not omit_resids
If the receptor is not chain A you need to change selections in the rest of the pml script file (e.g. show cartoon, selection).
When you are satisfied with the view, generate the image and save it to your hard disk:
util.performace(0) ; #this corresponds to: Menu: Display,
Quality, Maximum quality
Zoom the image, such that it fills the vertical dimensions of your PyMOL
graphics window. Start with command: "draw 1000,1000". Shift the
structure (middle mouse button pressed) to the center and adjust the y
pixel value of the "draw x,y" command such that the structure fills the
complete image and is centered.
Save the image to a file which has the same root name as your pml script:
png my_image.png
If not available as linked protoss protonated structure here, use
proteins.plus to download and add hydrogens.
4eiy, the
structure of the adenosine receptor that we used already a lot.
7yon, a cryoEM structure with a peptide agonist (large ligand, difficult).
7piu, cryo-EM structure of the agonist setmelanotide bound to the active
melanocortin-4 receptor (MC4R) in complex with the heterotrimeric Gs
protein at 2.6 A resolution.
3rfm, thermostabilised adenosine A2A receptor in complex with caffeine
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