Re: [Jmol-users] Selecting molecules in unit cell -Jmol 11

[Bob H. <ha...@st...>]

Ah, I see. If they do not cross cell boundaries, you could

select cell=566 and ....

for example. Or, if not, and they are all connected as a single organic 
molecule, you could:

select within(molecule,cell=566 and symop = 1)

"site" is crystallographic site, so that might also be useful.

I don't think there is a general solution. Is this a specific problem or 
a general one?



Patrick J. Carroll wrote:

>Bob,
>         The difficulty I have in selecting molecules in the unit cell is 
>that I would like to be able to, e.g., select the molecule produced by the 
>symmetry operation X, 1/2-Y, 1/2+Z and THEN select the one produced by 1+X, 
>1/2-Y, 1/2+Z, which is the same symmetry operation, just translated +1 in 
>a. But when I select symop=2, all of the symop=2 molecules (1+X, 1/2-Y, 
>1/2+Z, X, 3/2-Y, 1/2+Z, X, 1/2-Y, 3/2+Z, etc) are selected. I, maybe, could 
>select by molecule no., if I knew the relationships between the molecule 
>nos. and the sym op's (and I am ignoring, for now, the problem of the Jmol 
>"molecule" not being the same as the "crystallographic molecule", usually 
>called, BTW, the "asymmetric unit").
>
>
>Pat Carroll
>Chem Dept
>U of Penn
>
>
>
>
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