Skip to content
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.
Emacs Lisp
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
doc Add new screenshots! Apr 12, 2015
LICENSE Initial commit Sep 15, 2014
README.md
pdb-mode.el Add rna-puzzle-ready [in testing] Aug 15, 2017

README.md

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.

emacs-pdb-mode & rna-pdb-tools

rna-pdb-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-pdb-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:

screenshot

.. change Chain ID:

screenshot

Send a part of the PDB file directly to PyMOL:

screenshot

You can’t perform that action at this time.