[Chimera-users] Duplicate Atom Serial Numbers

Albion Baucom baucom at msg.ucsf.edu
Thu Nov 16 15:46:31 PST 2006

When I generate a PDB file, and generate symmetry related biological  
units, I frequently replicate the single structure. When I do this  
the atoms numbers get duplicated and when I open the structure in  
Chimera it prints to the screen

warning: duplicate atom serial number found: NNNN

where NNNN is the duplicate number.

The problem with this is it slows down opening the file by a huge  
factor. I assume that the print statement to the terminal is adding a  
lot of time to the file reading process.

Is there any way around this, or a way to simply turn this off? I am  
not concerned with the specifics of the duplicate atom numbers. A  
single error message to alert me the fact that there are duplicate  
atoms would be enough.

Once Chimera is done reading the structure it works fine. Rotations  
are smooth. Displaying ribbons is quick, etc. This doesn't appear to  
be a slow down due to atom limitations, but simply the overhead of  
printing that error message over and over to the console.

Of course I am aware that there are BIOMT records to generate  
symmetry related molecules using a single repeating unit, or I could  
generate separate PDB files for each repeating unit, but this is a  
lot more work and bookkeeping when I can use some existing simple  
programs to simply rotate and translate a single set of coordinates.



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