Matrin,

set retain_order

before loading the input PDB file.

Depending on the application, you may also wish to 

set pdb_retain_ids

Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
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> -----Original Message-----
> From: [email protected] 
> [mailto:[email protected]] On Behalf 
> Of Martin Höfling
> Sent: Thursday, April 24, 2008 11:13 AM
> To: [email protected]
> Subject: [PyMOL] Keeping PDB ordering
> 
> Hi all,
> 
> is there a simple way to prevent reordering of atoms and 
> insertion of additional TER records by pymol? I have a 
> protein embedded in a bilayer with tip4p water, where this 
> occurs when I delete parts and export the rest of the System.
> 
> Best wishes
>       Martin
> 
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