[Chimera-users] problem with huge PDB atom numbers

Elaine Meng meng at cgl.ucsf.edu
Tue Feb 16 10:14:47 PST 2010

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  

I'm not sure what the upshot will be, but it is useful to know about  
these problems.  Thanks for letting us know,
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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