Molecules should have named Empties

[zeffii]

should this be happening inside core_EmptyChainsCreation() ? this doesn't appear to be making any Empties, has this ever worked?

[MonZop]

The Empty was introduced in the latest version: The idea was to have an Empty that can be used to 'govern' the entire molecule (rotate and translate), independent of the internal movements (atoms). This has become important only thanks to the possibility of importing more than one protein in a single Blender file. Therefore the Empty should have as dependencies the sruface, with its features, the lines of the EP, and all the atoms.

[zeffii]

Within the entire 'atom cloud' (as I call it) described by the pdb, there are various levels of molecules going from the simplest bonded atoms of one type of molecule, to compounds to bigger structures like Nucleotide..etc . Is it just the entire atom cloud that needs an empty or each of the tagged molecules listed in the pdb?

I think this ties in with the feature which lets you select other atoms of a molecule

[MonZop]

My suggestion would be that an Empty is associated to the single molecule: if the PDB contains > 1, then BioBledner might want to build >1 'atom clouds'. However, this will imply that the user knows what she's doing. For example: the file 03_3IV5_DNA_proteinComplex contains 4 molecules: the two DNA strands (C and D) and the two parts that compose the Fis protein (A and B), which is functionally a dimer, i.e. it works as a pair of chains (like the scissor, just to make an example). There is no way for BioBeldner to know that the DNA will stay paired and that Fis does not work as a monomer; it is the user that must take care of not disrupting the functional unit.

Therefore BB should build 4 Empties: plexA, plex B plexC and plexD (in case the 4 letters of the file name are kept). The used might then build another empties that keeps the protein (A and B) and the DNA together