[Molvis-list] no chain designation

Gale Rhodes rhodes at usm.maine.edu
Wed Nov 17 11:59:23 EST 2004

On Nov 15, 2004, at 9:58 AM, Roberts, Rebecca wrote:

> Hello -
> I've got a molecule that has a propeptide but there are no chain 
> designations in the file to distinguish this part of the molecule from 
> the rest. So, when selecting a region (I'm trying to select only the 
> first 62 amino acids that consistitute the propiece) PE selects the 
> first 62 and also the next 62 (because the residue numbering system 
> begins again from '1' at the '63rd' amino acid). Any ideas on how to 
> get around this when no chain designations are provided?

Hi, Rebecca!

DeepView (also known as Swiss-PdbViewer) has a tool that is helpful for 
changing chain, residue, and hetatm designations in PDB files. It's 
somewhat hidden under the command Edit:Rename Current Layer. The dialog 
for the command allows you to add or change a chain designation for 
selected residues in the currently displayed layer, as well as to 
renumber selected residues. It is also possible to merge different 
layers into a single layer and save it as a PDB file. (A layer is one 
of the currently loaded models -- DeepView can handle many models at 
once, superimpose them, and move easily among them.) DeepView writes 
very well-behaved PDB files that retain all atom designations and 
usually work well in other programs.

For more about DeepView, see




Hope this is useful.


Gale Rhodes, Professor of Chemistry
University of Southern Maine
PO Box 9300
Portland, Maine 04104-9300

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