Piero,
Try this for now as a Jmol script.
function zAdd(type, dist, a, ang, b, tor, c) {
/*
adds an atom x connected to A and distance DIST from A
with angle ANG for x-A-B and dihedral TOR for x-A-B-C
Note: If a or b or c is a coordinate, such as {1 2 1},
and we have fractional coordinates, then those will be ASSUMED
to be fractional. Do not use fractional notation {1 2 1/1} for a, b, or c.
Instead, if you must use cartesian coordinates, add ".fxyz" to that:
zAdd("H", 1.0, {atomno=1}, 109.5, {atomno=2}, 60, {1.5 2.4 3.2}.fxyz)
*/
var vbc = c.xyz - b.xyz
var vba = a.xyz - b.xyz
var p = a.xyz - (vba/vba) * dist
var mol = "1\n\n" + type + " " + p.x + " " + p.y + " " + p.z
var p = a.xyz + cross(vbc, vba)
set appendNew false
load append "@mol"
var newAtom = {*}[0]
connect @a @newAtom
rotate Selected molecular @a @p @ang @newAtom
rotate Selected molecular @b @a @tor @newAtom
}
load caffeine.xyz
zAdd("H",1,{O11}, 109.5, {C5}, 60, {n4})
On Mon, Oct 18, 2010 at 8:45 AM, P.Canepa <[email protected]> wrote:
> Dear all,
>
> have you ever thought about the possibility to add an option to Jmol which
> adds
> extra atom following the z-matrix procedure?
> Thanks, Piero
>
>
>
>
> --
> Please consider the environment before printing this e-mail.
>
> Pieremanuele Canepa
> Room 104
> Functional Material Group
> School of Physical Sciences, Ingram Building,
> University of Kent, Canterbury, Kent,
> CT2 7NH
> United Kingdom
>
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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