[Chimera-users] Weird looking stretch in ribbon presentation

Boaz Shaanan bshaanan at exchange.bgu.ac.il
Fri Mar 29 17:11:38 PDT 2013

Hi ,

I came across a weird looking stretch when I use ribbons presentation (latest build x86_64, 38529, 27/3/13). Please check it yourself. In the entry 2pan, if you select residues  114-115 (Phe-Gln) and a few residues before and after in any chain (well, I checked C & D, I guess it's the same for all chains) and use ribbons + side-chains presentation the Ca-Cb gets very long compared to backbone+side-chain presentation (the Cb's are in the same place in both presentation, of course). In fact, the ribbon trace is shifted away from the backbone really is, hence the Ca-Cb bond gets excessively long.  It probably has to do with the shape of the turn in this stretch and the way the ribbons are calculated. However as this is an important region for my analysis it drew my attention by its weirdness. Is there no remedy for this?


Boaz Shaanan, Ph.D.                                        

Dept. of Life Sciences                                      

Ben-Gurion University of the Negev                          

Beer-Sheva 84105                                            



E-mail: bshaanan at bgu.ac.il

Phone: 972-8-647-2220  Skype: boaz.shaanan                  

Fax:   972-8-647-2992 or 972-8-646-1710    

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