[Jmol-users] display of secondary structure elements

[William R. <whr...@ms...>]

Hello All,

I have been converting a collection of Chime displays into Jmol format 
with general success, but I have encountered a puzzling behavior with 
some peptide and protein secondary structures. If anyone has experienced 
similar results I would appreciate your comment.

  To illustrate, I have prepared a page comparing Chime and Jmol 
rendering of a few cases.
  The url is:  
http://www.cem.msu.edu/~reusch/Test/Peptides/peptcomp.html 
<http://www.cem.msu.edu/%7Ereusch/Test/Peptides/peptcomp.html>

The pdb files come from different sources and exhibit identical displays 
in Rasmol (v 2.6) and Chime. You should be able to download copies from 
this site without difficulty. Briefly, Chime shows both sheet cartoons 
and helix ribbons for lysozyme, but Jmol displays only the helices. The 
small beta-sheet model does not display either H-bonds or sheet cartoons 
in Jmol, but both are shown with Chime (& Rasmol). Curiously, 
chymotrypsin fails to show helices or sheets in the larger protein 
segment with Chime, whereas, Jmol displays a complete assortment 
throughout the structure. Although I have not incorporated it in the 
example, the color chain command in Chime (& Rasmol) identifies four 
distinct segments in the chymotrypsin structure, but only two are 
identified in Jmol. Most of the Protein Data Bank files I have examined 
behave well in both displays. However, the very large protein ricin 
loads in Chime, but will not load in Jmol.
My testing has involved Wintel platforms running I.E (v 5 & 6), as well 
as Netscape and Mozilla (Chime does not work); and Macintosh G3 and G4 
platforms running OS 9.2 and 10.3.

Bill