emacs-pdb

pdb-mode is an emacs-lisp minor mode for Emacs to perform a number of useful editing functions on Protein DataBank (PDB) formatted files. XEmacs and/or GNU Emacs are available for most computing platforms.

Read more on implemented functions https://crystal.scb.uwa.edu.au/charlie/software/pdb-mode/

(@mmagnus: I'm not an author of this code, I just updated it slightly, fixed it in 2020, all credits go to Charlie Bond & David Love, I asked Charles S. Bond if I can share it and he was OK with that ;-)

emacs-pdb-mode & rna-tools

rna-tools can be used side-by-side https://github.com/mmagnus/emacs-pdb-mode to edit files structural files in the PDB format.

http://rna-tools.readthedocs.io/en/latest/emacs.html

Install

My installation config:

  ;; pdb.el
  (load-file "~/.emacs.d/plugins/pdb-mode/pdb-mode.el")
  (setq pdb-rasmol-name "/usr/bin/pymol")
  (setq auto-mode-alist
       (cons (cons "pdb$" 'pdb-mode) 
             auto-mode-alist ) )
  (autoload 'pdb-mode "PDB")

How to customize the colors?

You can play around with:

(make-face 'pdb-key1-face)
(set-face-background 'pdb-key1-face "dim gray")
(make-face 'pdb-comment-face)
(set-face-foreground 'pdb-comment-face "dark gray")

.. a full list of Emacs color you can get by typing M-x list-colors-display.

Select a residue:

.. change Chain ID:

Send a part of the PDB file directly to PyMOL: