[Chimera-users] problem with huge PDB atom numbers

Michael Zimmermann michaelz at iastate.edu
Tue Feb 16 10:51:50 PST 2010

I'm sure many of you are aware of this, but just in case some are not
I thought I'd mention that the PDB is working on a new file format
that will accommodate these large structures.  I don't know what their
thoughts are exactly, but they tell me that it will make the "split
entries" obsolete.

On Tue, Feb 16, 2010 at 12:14 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Sam,
> The spillover into column 6 was intentional, but it is understandable that
> it could cause problems for other programs.  The original PDB format (as you
> must be painfully aware) was not designed to handle such large structures as
> we have today, and different programs have taken different liberties with
> the format to try to accommodate these things.  PDB itself has taken the
> approach of splitting large structures into multiple entries.  Your approach
> breaks the rule of unique serial numbers, and Chimera's approach messes with
> column 6.  Chimera can use the serial numbers as unique identifiers, and if
> I remember correctly, we started using column 6 after noting that another
> program (maybe it was AMBER trajectories?) expanded large serial numbers
> there.  Conversely, the programs you are using apparently tolerate duplicate
> serial numbers but not numbers in column 6.
> I'm not sure what the upshot will be, but it is useful to know about these
> problems.  Thanks for letting us know,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Feb 14, 2010, at 1:00 PM, Samuel Coulbourn Flores wrote:
>> Hi Guys,
>> I thought I'd point out a problem with Chimera's atom numbering.  I am
>> working on a ribosome model which has about 50 chains.  The ribosome pushes
>> the limits of the PDB format;  the five columns reserved for atom numbers
>> are not sufficient to give each atom a unique atom number.  This is not
>> typically a problem for me, I just start the atom numbering at 1 for each
>> chain.  However chimera doesn't do this, it tries to assign sequential,
>> unique numbers to each atom and ends up spilling over onto column 6, which
>> is in the record name field.  This wreaks havoc with other programs which I
>> use to process the PDB files that chimera puts out.  I am manually
>> renumbering to deal with the issue, but the developers should think about a
>> more permanent solution.
>> Sam
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Michael Zimmermann
Ph.D. student in Bioinformatics and Computational Biology
Department of Biochemistry, Biophysics and Molecular Biology
Iowa State University

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