[Chimera-users] ribbon problem
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 Pettersen
> 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 <mailto:Chimera-users at cgl.ucsf.edu>
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