
Hi, The problem opening the biological unit PDB file for virus capsids 1aym and 1p5y is that you are running out of memory. The asymmetric unit is small 1aym (human rhinovirus 16) 7000 atoms 1p5y (canine parvovirus) 4400 atoms but with the 60-fold icosahedral symmetry, these become 420,000 atoms and 264,000 atoms. Chimera requires about 2-3 kbytes per atom, so you will need a computer with at least 1 Gb and preferably 2 Gb of physical memory to open these. With less memory the machine will become extremely slow as it uses your hard-disk to cache data that won't fit in the physical memory. I opened the 1aym biological unit on a Mac desktop machine which has 1.5 Gbytes of physical memory in a few minutes. Chimera was using about 1 Gbyte after it opened. To open the model with less memory you could make a new PDB file containing only the CA backbone atoms, or just CA, C, N, and O backbone atoms. That would require writing a script to filter out the other lines of the file. We could give you the backbone only files if you want. Another approach is to just open the asymmetric unit and use the Chimera multiscale tool (Tools / Multiscale / Multiscale Models) to make the 60 copies. This does not copy all the atoms so it does not need alot of memory. You open the asymmetric unit and press the "Make models" button at the bottom of the Multiscale dialog to display the full capsid. Here are images of 1aym and 1p5y I just made this way: http://www.cgl.ucsf.edu/home/goddard/temp/1aym.png http://www.cgl.ucsf.edu/home/goddard/temp/1p5y.png You can also show some of the capsomeres as ribbons or all atom displays. But if you use Multiscale and try to show the full capsid at atomic or ribbon level, then it will try to copy the asymmetric unit 60 times and you will again need alot of memory. More images of virus capsids using the Multiscale tool are on our web site http://www.cgl.ucsf.edu/Research/virus/ and on the VIPER web site http://viperdb.scripps.edu/ Tom