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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

----- Elaine C. Meng, Ph.D. meng@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

Thanks Elaine, Tom. This is of course for "quick and dirty" helical structures where I want to take a single chain and replicate it dozens of times while imposing symmetry to create a short segment of a fiber. The MODEL and ENDMDL are good suggestions, as well as the /dev/null redirect. I suppose there are scenarios when one would want to know about duplicate atoms, but in my case there are just so many that it is pointless to print them all out. The ultimate solution here is really for me to not to be so lazy ;) As an aside, I typically use the program pdbsymm which is included with the SITUS package to impose the symmetry to generate an arbitrary number of symmetry mates along a helical axis (using polar coordinates). It simply replicates the original PDB file while updating the coordinates, thus I have the duplicate numbering problem. But your suggestions should do the trick in the meantime. Thanks again. Albion