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