Re: [Jmol-users] pseudo atoms in an SD file

[A. H. <ang...@ua...>]

Hi Rajarshi 

1. The standard element-id for "unknown" atoms in Jmol is Xx. You may use that and select 
them successfully using e.g. "select _Xx"  (I've had some trouble with this syntax before, but 
don't remember the final solution; I may search and dig it up if you need so)

2. I'd bet (but haven't tested it) that you can use any id for your dummy atoms --as long as it 
is not an existent element symbol, Jmol will treat them as unknowns, give them the default 
pink color and default small radius, but you should be able to select them by "element" 
name, such as e.g.  "select _R".
However, my experience with this is mostly in PDB format; I am not sure if it will behave the 
same with SD (or MOL) format.

3. If you manage to use custom symbols, then you may be able to assign them different 
default colors using "color _R green" and even radii in a less direct way which I cannot say 
right away.