[Molvis-list] pdb-l: working with a file with two models superimposed

Michael Sternberg sternberg at anl.gov
Mon May 12 18:45:00 EDT 2008

On May 12, 2008, at 12:49, Kevin Karplus wrote:
> In rasmol,
> 	help primitives
> 	help expression
> will explain (somewhat awkwardly) how to select models in rasmol.
> [..]
> For example, I wouldn't mind seeing a primitive that allowed
> specifying an atom by number, as they are reported when clicked on.
> That is, it would be nice to have
> 	select atom 114 and */1
> to get
> Atom: CB 114  Group: TYR 16  Chain: A  Model: 1

Ahh - Rasmol has this already, though the help for it in a somewhat  
obscure place:

	help comparison
	atomno == mmm
	atomno >= mmm and atomno < nnn

As I hardly ever handle biomolecules, I am not sure if atom numbers  
in them are global or per chain.

Caution:  In .xyz files, atom numbers are assigned internally,  
starting from 0 (fine with me), in for .alchemy files the numbers are  
imported from the file; when I create alchemy files (mainly to force  
bonds), I start numbering from 0 as well.

Now, here's what really would rock:  arithmetic expressions based on  
coordinates, e.g.:

	x + y > 0

Regards, Michael

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