[Molvis-list] no chain designation

Eric Martz emartz at microbio.umass.edu
Wed Nov 17 15:29:41 EST 2004

I have made an entry under free software at molvisindex.org for Annemarie 
Honegger's PDB Excel macros, so in future it will be easy to find them.

Here are a couple of more options in addition to the excellent suggestions 
already posted.

1. DeepView: Edit, Rename Current Layer can (a) give a new chain name to 
the selected residues, and/or (b) renumber the selected residues with a 
specified starting number. Thus one could renumber one of the two 1-62 sets 
as 101-162, or give them a different chain name (causing Chime to fail to 
display the covalent bond between "chains"). The layer can then be saved, 
and optionally the lines in the saved PDB file inserted by DeepView can 
easily be deleted with a text editor. They are bulky but harmless for 
non-DeepView software, and useful within DeepView (e.g. they maintain the 
selection at the time the layer was saved). The saved files work fine in Chime.

For Protein Explorer, such a modified file can be put on any server, and 
displayed in PE either by pasting the URL in the long slot at the FrontDoor 
(click on the link "molecule's URL" below the short slot for PDB codes), or 
by creating a link to the modified file (click on the link "Create 
hyperlinks that prespecify molecules" also below the PDB ID slot). PE's 
Atlas of Macromolecules has many examples of links to such modified PDB 
files, e.g. under toxins, the heptamer model,

2. RasMol's "renumber" command renumbers residues in all chains in the 
currently loaded PDB file, and optionally accepts a starting value (which 
can be negative). But CAREFUL! RasMol (2.6 only?) unconditionally changes 
all coordinates by providing its own arbitrary origin. Therefore one CANNOT 
separate multiple chains into different PDB files, renumber and save each, 
then concatenate them. If you did, the chains will no longer have the 
proper distances from each other (may even occupy the same space). 
Therefore DeepView is better for renumbering. For a summary about this 
behavior, see http://www.umass.edu/microbio/rasmol/pdbtools.htm

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Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US  413-545-2325/FAX 413-545-2532
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