VMD-L Mailing List

From: Avell Diroll (avelldiroll_at_yahoo.fr)
Date: Wed Mar 07 2007 - 17:39:38 CST

Axel Kohlmeyer wrote:
> On Mon, 5 Mar 2007, Esther Brugger wrote:
> EB>(snip)
> EB> I met a weird problem when I read a pdb file using VMD.
> EB>(snip)
> EB> I use Copy/Paste command in Nedit editor, VMD couldn't recognize the
> EB> PDB file. I really don't know why.
>
> the pdb format is pretty strict in terms of column alignment.

Indeed

> the safest way to rename groups of atoms with the same properties
> is to use atom selections within vmd to do it and then have vmd
> write out the modified .pdb file.

I definitely agree, but sometimes using a text editor might be
quicker/compulsory to edit a pdb file. I found a few years ago a _great_
pdb extension mode for emacs that ease the task of editing such files.
(as an example, the columns are shown when the file is rightly formatted)

The extension is available on the author's website (author: Charlie Bond):
http://stein.bioch.dundee.ac.uk/~charlie/software/pdb-mode/pdb-mode.html

Bye the way, no emacs arcane knowledge are mandatory to use this
extension ... and this is coming from a vim user.

HTH
Cheers,

Julien