Results 2.0

This is probably due to your molecular viewer. Some molecular viewers do not have support for multiple PDB entries in one file. There are two choices for how to proceed. The first is to switch to a molecular viewer that supports multiple entries in a single file like PyMOL. The second choice is to split the model file into receptor and ligand and load those independently into your viewer. On Linux and Mac OS X, you can do this by calling file=model.000.00.pdb;csplit --prefix=${file/pdb/} --suffix-format='%02d.pdb' $file %HEADER% /HEADER/ , substituting your chosen model for model.000.00.pdb. This should give you two files, model.000.00.00.pdb and model.000.00.01.pdb, that contain the receptor and ligand respectively. On Windows, you can open the file in Notepad or Notepad++, searching for the END record in the middle of the file and manually copy the two halves into separate files. Alternatively, simply removing the lines that say END may allow your viewer to load both the receptor and ligand into one object. On Linux and Mac OS X, this can be done by calling grep -Ev '^(HEADER)|(END)' model.000.00.pdb > model.000.00.stripped.pdb . On Windows, you can manually remove those lines in one of the text editors mentioned above. (If you have a simple way to do either of these that is built into Windows, we would love to hear about it.)