[Chimera-users] ribbon problem
pett at cgl.ucsf.edu
Thu Sep 23 12:47:38 PDT 2010
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
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.
UCSF Computer Graphics Lab
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.
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
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