VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Mon May 30 2011 - 00:33:50 CDT

Oemer,

The script I sent you in my previous email is wrong ...

Here is a working version which you can further modify to exclude lines
that begin with "END" or "CRYST" :

set file [ open filename w ]
set a [ atomselect $molid1 all ]
set b [ atomselect $molid2 all ]
$a writepdb a.pdb
$b writepdb b.pdb
set f1 [ open a.pdb r ]
set f2 [ open b.pdb r ]
set data1 [ read $f1 ]
set data2 [ read $f2 ]
lappend data [ split $data1 "\n" ]
lappend data [ split $data2 "\n" ]
puts $file $data
file delete a.pdb
file delete b.pdb

Vlad

On 05/29/2011 09:53 PM, Vlad Cojocaru wrote:
> Oemer,
>
> 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"
>
> Vlad
>
> On 29.05.2011 16:14, Ömer 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]mpi-muenster.mpg.de
> 

-- 
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]mpi-muenster.mpg.de