[Chimera-users] ribbon problem

Conrad Huang conrad at cgl.ucsf.edu
Mon Sep 27 17:39:26 PDT 2010

I've added some ribbon code to handle circular structures.  Both the 
original "cycle.pdb" file from bug report #2777 and pdb:2kux are now 
displayed properly.  I tried your frames2.pdb, but that still showed two 
ends.  I'm not sure if that is due to the incorrect connectivity in the 
file.  Can you download the latest daily build and see if it works any 
better with your trajectory input file?  Thanks.


On 9/23/2010 12:30 PM, Francesco Oteri wrote:
>    I've supposed the problem resides in the pdb, for this reason i tested
> the amber topology as input.
> Using amber, in fact, the correct bonds are displayed.
> Nevertheless, the ribbon is still cutted. I saw that it is a bug and
> that a new entry in the bugzilla has been opened.
> Il 23/09/2010 20:31, Elaine Meng ha scritto:
>> 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.
>> Best,
>> Elaine
>> ----------
>> 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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