Re: [Jmol-developers] internal coordinates?

[Miguel <mi...@jm...>]

> internal coordinates SHOULD be very easy to use, particularly if they are
> handed
> to you and you don't have to generate them yourself. They are amazingly
> concise.

We are already handling fractional coordinates, so adding another
coordinate system will not be difficult ... IF ...

> The only complication I can imagine is that they sometimes involve
> "phantom" or
> "temporary" atoms for starting points.
>
> For example, in this example we have a first atom at 0,0,0, then two
> phantom
> atoms on roughly perpendicular axes. They define the starting point for
> the next
> dihedral, and you are off and running. Mostly QM programs start with these
> so as
> to define positions when symmetry is an issue.
>
>    ATOM    CHEMICAL     BOND LENGTH    BOND ANGLE    TWIST ANGLE
>   NUMBER    SYMBOL      (ANGSTROMS)    (DEGREES)     (DEGREES)
>     (I)                   NA:I          NB:NA:I       NC:NB:NA:I       NA
>   NB
>     NC
>      1       C(  1)        0.000000      0.000000       0.000000
>
>      2      XX(   )        4.117293      0.000000       0.000000        1
>
>      3      XX(   )        2.303156     90.000000       0.000000        2
>    1
>
>      4       C(  2)        1.351924  * 133.488008  *  180.000000  *     1
>    2

... IF ... there are three floats per atom.

Q: Is it the case that there are only 3 numbers per atom? bondLength,
BondAngle, and TorsonAngle?

Q: What are NA, NB, and NC?



Miguel