From: Vlad Cojocaru (
Date: Sun May 29 2011 - 14:53:11 CDT


You have 2 solutions:

1) save each molecule separately and cat them together in the shel

2) Write a small script such as

set file [ open filename w]
set a [ writepdb [ atomselect $molid1 all ] ]
set b [ writepdb [ atomselect $molid2 all ] ]
puts $file "$a"
puts $file "$b"

and run it as "vmd -e $script"


On 29.05.2011 16:14, Ímer AN wrote:
> Hi,
> Is there any option to "Save Coordinates" of all loaded molecules at
> once, preferably merged in a single pdb file if possible?

Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]