[Chimera-users] Duplicate Atom Serial Numbers

[Elaine Meng]

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.
Best,
Elaine

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
                      http://www.cgl.ucsf.edu/home/meng/index.html