Hi Thomas, Well, I wouldn't call it a problem… it just happens that Pymol does one thing and Chimera does another. Chimera "knows" they are multiple chains, however. If you want the chains in different colors, for example, you could use the command: rainbow chain You can also specify the colors to use in this command. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/rainbow.html> It doesn't have anything to do with the HEADER. This file only has one HEADER line, and it just contains the name of a PDB file. The chain IDs are in the ATOM lines. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jan 13, 2014, at 5:18 PM, Thomas Hrabe <thrabe@sanfordburnham.org> wrote:

Hi everyone, I believe I found a problem with the >HEADER< keyword in PDB files. Some programs may create pdbs with the header keyword specifying the origin or a name of a chain or other metadata with the coordinates below. PyMol understands this keyword and colors chains that have identical chain ID (see example attached) in multiple colors while chimera interprets all as one chain. Thanks, Thomas