I personally prefer to export a publication-quality image of the desired view of the molecule without labels and then place the labels in a general-purpose graphics program such as gimp or photoshop. However, if you insist on doing it all within PyMOL, use the command line for best control.

First, find exactly the the representation and orientation of the molecule you want to show, and save it!

Do get a white background, specify:

bg_color white

To color the labels black, use:

set label_color, black, (selection) (https://pymolwiki.org/index.php/Label_color)

Using a selection, you can use different label colors for different objects

Normally, you label the Calpha positions:

label n. CA, "%s, %s" % (resn, resi) (https://pymolwiki.org/index.php/Label)

You might want to not label all Calpha positions, but only a subset

If you select the residues you want to label by clicking on them, set "selecting" to C-alpha, select the residues you want to label, then specify

label sele, "%s, %s" % (resn, resi)

On page https://pymolwiki.org/index.php/Label you also find the commands you need to set the size and font of the labels

By default, the label appears centred on the atom you are labeling. With the command:

set label_positions, (x, y, z) (https://pymolwiki.org/index.php/Label_position)

you can offset the label the label in the horizontal (x) and the vertical (y) direction,

and move it towards you (z) to make sure it is not hidden by other parts of the molecule

Pymolwiki is your friend - to find out how to do something in pymol, e.g. to label,

google "pymolwiki label" to find the commands related to that specific action.

I would suggest you to use the software chimera or DS visualizer to get good images for your protein-protein interactions.

Annemarie Honegger Thanks a lot for your suggestion, I will try the same.

Annemarie Honegger, I understood the code to label, but I am still struggling to visualize the protein-protein interaction in a better way so that I can label the interacting residues. I have run InterfaceResidues.py but didn't get anything in the result. Can you please suggest me any other way to perform the same?

Assuming you have two selections, protA and protB, representing the two proteins. You can then use the "within" selection to select atoms or residues in one protein that are within a given distance of the the second protein.

To select for VdW contacts (in a structure without explicit hydrogens) you would specify: (https://pymolwiki.org/index.php/Selection_Algebra)

select interA, protA within 3.6 of protB

you could then expand the selection to the residues that contain at least one contact atom with the byres selection, short br. and display the residue:

show sticks, br. interA

For more, see my presentation "Intermediate PyMOL" (Presentation Intermediate PyMOL

You also may first want to read Article An Introduction to Biomolecular Graphics

Check this https://youtu.be/uor-um6l5PI check this link might be useful

Same problem.Any solutions?

Hello Hiteshree Buch , Md. Mahfuzur Rahman Bhuyan !

I have exactly written a step-by-step blog on medium on how to visualize protein-protein docking in PyMOL.

You can find the blog post at: https://medium.com/@snippetsbio/visualizing-protein-protein-docking-using-pymol-cc49494e54bb

Let me know if this helped you!