[Molvis-list] no chain designation

[Gale Rhodes]

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

http://www.usm.maine.edu/~rhodes/SPVTut/index.html

and

http://spdbv.niehs.nih.gov/

Hope this is useful.

Cheers!

Gale Rhodes, Professor of Chemistry
University of Southern Maine
PO Box 9300
Portland, Maine 04104-9300
http://www.usm.maine.edu/~rhodes