Re: Coordinate Output in both binary and ASCII. Or converting binary to ASCII in the command line

From: Leandro Martínez (
Date: Mon Mar 02 2009 - 11:02:08 CST

It seems that you know already the VMD command syntax, so write the sequence
of commands to a file (lets call it script.vmd), and run vmd with:

vmd -dispdev text -e script.vmd

This will do all the operations you want in "command line" mode, that means,
with no graphical interface, and
then can be scripted and run in background.

For example, this simple script opens a pdb file, sets the B-factors of some
atoms to something different than zero, writes a new pdb file and exits:

mol new protein.pdb type pdb first 0 last -1 step 1 filebonds 1 autobonds 1
waitfor all
set sel [ atomselect top "segname PROT and name CA" ]
$sel set beta 1
$all writepdb newfile.pdb


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