[Chimera-users] ribbon problem

Francesco Oteri francesco.oteri at gmail.com
Thu Sep 23 13:05:23 PDT 2010

  As I told to Elaine,
i know the problem about  pdb file, for me is not a problem reordering 
it. Nevertheless, the problem remains: using amber topology I don't see 
a continue ribbon.
I'll wait for the fixing of this bug.

Thanks for your help

Il 23/09/2010 21:47, Eric Pettersen ha scritto:
> Hi Francesco,
> As Elaine mentions, as per the PDB standard the chain connectivity of 
> standard residues (i.e. residues in ATOM records) is implied by their 
> order in the file, barring TER records between the residues.  This is 
> why Chimera is producing those longs bonds.  For example, your file 
> has residues 300 and 301 one after the other in the PDB file without a 
> TER card, so Chimera connects them despite them being >50A apart. 
>  What you really need to do is reorder the file so that it is in 
> connectivity order.
> Also, the file was seemingly made by trjconv, which AFAIK is a program 
> for converting Gromacs trajectories to PDB format.  I thought you were 
> using an Amber trajectory.  Why aren't you using ambpdb, which 
> directly converts Amber trajectories to PDB files?
> Lastly, trjconv is doing a bad job with justification of hydrogen 
> names in the 4 columns alloted to the atom name.  It does well with 
> some names, like "1H2*" and " H3*" (so Chimera can deduce the element 
> type from the first two columns) but then outputs some stinkers like " 
> 1H7" and " 2H7".  Sigh.
> --Eric
>                         Eric Pettersen
>                         UCSF Computer Graphics Lab
> http://www.cgl.ucsf.edu
> On Sep 23, 2010, at 11:31 AM, Elaine Meng wrote:
>> 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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