VMD-L Mailing List

From: Ignacio Fernández Galván (jellby_at_yahoo.com)
Date: Wed Nov 17 2010 - 12:30:59 CST

----- Original Message ----
>> Finally, if any one could tell me how to get more information about the atom
>> selection using :"and" and "or" it would be great because in the manual I
>> did not find much.
>
> there is not much about it. they work like logical operators
> in many other script languages.

You just have to keep in mind that "and" and "or" do not combine selections, but
conditions that selected atoms must satisfy. Thus, "nucleic and resname THY"
does not select all atoms in a nucleic acid plus all atoms in a THY residue, but
all atoms that are both a nucleic acid and a THY residue. Since you probably
don't have any THY residue that is not a nucleic acid, that's actually
redundant.

I've seen some novices have a bit of trouble with this and, for instance, try to
select a protein and all water molecules with "protein and water", which, of
course, results in nothing, as it actually means "all atoms that are both part
of a protein and of a water molecule", and what they really mean is "protein or
water".

I hope that help,
Ignacio