[Chimera-users] ribbon problem

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 23 11:31:38 PDT 2010

Hi Francesco,
Wow, this is a very pretty structure!  However, the PDB looks somewhat messed up.  Perhaps using the AMBER files solves most of these problems.

In PDB format, I believe the biopolymer (nucleic acid or protein) residues are connected by their order in the file, unless a break is enforced with TER.  However, the order in this PDB file seems to be quite different than what it should be, for the correct connectivity.  Residue 75 is very far from 76, 150 is very far from 151, etc. every 75 positions.  I tried just putting TER after every 75 residues, which does eliminate the very long bonds.  However, it seems like there may be other bonds that are supposed to be there that are not, and it would be necessary to do a lot of reorganization and renumbering of residues in this file to get the correct connectivity.  For example, it looks like maybe 76 is really supposed to be connected to 150, 75 is really supposed to be connected to 1, etc.

If there were correct ordering in the PDB file (and maybe this is already true for when you use the AMBER files as input), the Chimera limitation would give you just one break in each circular strand.  If this DNA is all one big circular strand, there should be only one break in the ribbon. 
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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