Hi Mahendra, Probably the format is slightly wrong for the lines with the calcium ion coordinates. For example, the name CA for the calcium ion should *not* line up with the name CA in the protein alpha-carbon lines. In the ATOM and HETATM lines of PDB files, <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coords> ...the ion name CA should be in columns 13-14, whereas the alpha-carbon name CA should be in columns 14-15. Misalignment of ion names is a common problem with the output of many programs. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#misalignment> Best, 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 Jul 30, 2012, at 9:21 AM, Mahendra B Thapa wrote:

Dear Chimera Users, I converted amber-12 generated rst-file in netCDF format [ test_equil.rst ] to the pdb format [ test_equil_rst.pdb] by using the cpptraj command of amber 12. When I loaded it in chimera, the protein structure looks fine but two calcium atoms that the protein binds could not be visualised, although the pdb file-format looks good. Let me help in this respect.