specifying surface model wrongly specifies its enclosed atoms

[Elaine Meng]

When I have atomic model #1 and its surfaces for chains A-D are models #1.1-4 (example: open 4hhb;style stick;ribbon;surf),

color #1.3 magenta

... (which as I understand it should only color the chain C surface) also colors all representations of the atoms enclosed in that surface, i.e. all "main" atoms of chain C. You can see it by then hiding surfaces (surf hide). The inclusion of chain C "main" atoms also happens with "select #1.3" and presumably other commands.

[goddard@…]

Apparently the atomspec code looks at if a specified model has an “atoms” attribute and if it does it considers those atoms to be specified.  MolecularSurface has an atoms attribute so atomspec uses those.

[Conrad Huang]

So what's the right thing to do? How do we make atomspec understand that a model should not be used to select atoms?