From: Axel Kohlmeyer (
Date: Mon Mar 22 2010 - 13:16:43 CDT

alternate suggestion (you may need to get v1.1 of the topotools package):

set sel1 [atomselect $mol1 {<enzyme selection>}]
set sel2 [atomselect $mol2 {<substrate selection text>}]

package require topotools

set mol3 [::TopoTools::selections2mol "$sel1 $sel2"]

animate write psf merged.psf $mol3
animate write pdb merged.pdb $mol3

this works for an arbitrary number of selections (unless you run out of memory).

please note that neither approach checks for atom overlaps.
therefore you have to choose your selections carefully.


On Mon, Mar 22, 2010 at 12:05 PM, John Stone <> wrote:
> Hi,
>  You may find it easier to first write out the structure that you move
> to a new file, and then simply use the "mergestructs" plugin, or merge them
> then move and write a new file, whichever works best for your intended purpose:
> Cheers,
>  John Stone
> On Fri, Mar 19, 2010 at 09:29:56PM -0700, Bernardo Sosa Padilla Araujo wrote:
>>    Hi All,
>>    I have two pdb files:
>>    -one of them with an enzyme and its substrate
>>    -the second one only has a very similar substrate( no enzyme)
>>     I want to load both pdbs, align the substrate from the second pdb to the
>>    substrate in the first pdb, and finally write a pdb file containing the
>>    enzyme (from the first pdb) and the substrate from the second pdb  but in
>>    the same position(with respect to the enzyme) as the substrate in the
>>    first pdb.
>>    I have in mind this script :
>>    #molecule 0 is the enzyme +substrate
>>    #molecule 1 is the other substrate
>>    #BAS is the resname of the substrate
>>    # Create a reference structure
>>    set ref [atomselect 0 "resname BAS"]
>>    # Create a selection to align
>>    set sel [atomselect 1 "resname BAS"]
>>    # Move molecule 1 onto molecule 0
>>    set all [atomselect 1 all]
>>    $all move [measure fit $sel $ref]
>>    In order to use writepdb I need to have everything in one selection, but I
>>    don't know how to put structures form different pdb in one vmd slection.
>>    Does anyone know how to do/circunvent this ?
>>    Thanks a lot in advance,
>>    Bernardo
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email:                 Phone: 217-244-3349
>  WWW:      Fax: 217-244-6078

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.