[Chimera-users] Duplicate Atom Serial Numbers

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 17 08:14:39 PST 2006

Hi Albion,
If you bracket each set of coordinates with the PDB records MODEL and 
ENDMDL (see NMR structures in the PDB, e.g. 1plx), Chimera will treat 
each set as a separate model and won't complain.

Another possibility is to use different chain IDs for each set, but 
that is a little more work.

On Nov 16, 2006, at 3:46 PM, Albion Baucom wrote:

> 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.
> Thanks
> Albion
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Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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