A common issue reported relates to problems saving or reading files that contain multiple molecules (in a single window) in DS.
Often the problems stem from attempting to save in pdb format. Here are two comments on this topic that I hope will help.
1) pdb files are intended only for multiple conformations of a single structure (think NMR structures). As a result there is not a method to save the names of different structures in a standard format pdb file. In my tests of four different molecules at all four structures _are_ saved and _do_ read back into DS fine. However, the molecule names are taken from the file name with the index number appended (original molecule name is lost). But, note, there is also a preference that will ignore all but the first molecule in a multiMolecule file containing multiple molecules.
There is also a DS preference that will cause the different entries in a pdb file to be loaded in as different "Conformations" -- similar to what you would get if you looked at a molecular dynamics trajectory.
(in case you ever wanted to do that):
Preferences / Molecule Window / Import / Create animation frm multiple molecules :
If you have this option selected AND the structures are the SAME molecule with only the conformations changing then you find that one molecule is loaded that contains one "Conformation" for each of the frames in the input file. In this mode only one frame can be viewed at a time but the results can be processed as if it were a trajectory. Note the “Conformations” tab in the data table at the bottom of the image shows the three input molecules (conformers).
NOTE, this preference should ONLY be active if the molecules in the file differ only by conformation, otherwise the results will be unpredictable. Therefore, it should always be turned off when not needed.
(2) Another way of saving multiple molecules that is not Accelrys proprietary is to use the .mol2 format. This can be read by most modeling programs and saves considerably more information than a pdb, including the names of each molecule with no restriction on the similarity of the molecules. This file format however will not save all information in the window, for example custom coloring or surfaces. To save all of the information in a window you should use the .dsv file format.
