Bob,
thanks for this. That was really fast! Now I will go and look if I can
create a menu entry for this...
Sebastian
Bob Hanson schrieb:
> Nico has released Jmol 11.3.27
>
> This release adds two new features and fixes a few bugs.
>
> vibrational vectors
> -------------------
> In labels, you can show the vibrational vector for an atom using
>
> %v gives x, y, and z
> %vx just x
> %vy just y
> %vz just z
>
> And in Jmol math you can use
>
> {atomno=3}.vibx
> {atomno=3}.viby
> {atomno=3}.vibz
>
> So, for example, the following function returns the atoms in XYZ file
> format translated by their vibrational vectors:
>
> function getVectors(modelNumber, scaleFactor);
> # return an XYZ file from a vibration;
> var theatoms = {model=modelNumber};
> var n = theatoms.size;
> var s = "" + n + "\n";
> s = s + "max vibration for model " + modelNumber + "\n";
> for (var i = 1; i <= n; i=i+1);
> s = s + theatoms[i].label("%e");
> s = s + " " +(theatoms[i].x + theatoms[i].vx*scaleFactor);
> s = s + " " +(theatoms[i].y + theatoms[i].vy*scaleFactor);
> s = s + " " +(theatoms[i].z + theatoms[i].vz*scaleFactor);
> s = s + "\n";
> end for;
> return s;
> end function;
>
> Then,
>
> x = getVectors(3,0.1)
> write VAR x "vib3a.xyz"
> x = getVectors(3,-0.1)
> write VAR x "vib3b.xyz"
>
>
> ---------------------------------------
>
> bondOrder command
> -----------------
>
> Jmol 11.2 introduced the capability to save the state, and part of that
> turns out to be the capability to define a bond order directly for a
> specific bond. The "bondorder" command was designed to do this; now I'm
> documenting it; Jmol 11.3.27 cleans up the command a bit.
>
> select *
> bondOrder single
>
> really this is the same as
>
> connect (*) (*) modify single
>
> One difference is that the bondOrder command also
> accepts numerical values. See
> http://chemapps.stolaf.edu/jmol/docs/?ver=1.4&command=bondorder
>
> Another difference is that if a set of bonds are chosen first, using
>
> select bond ({10,11,12})
> bondOrder 1.5
>
> then bondOrder acts DIRECTLY on that set of bonds. No reference to atoms.
> ({0}) is the first bond. Use at your own risk!
>
>
> -----------------------
>
> bug fixes
>
> --Function returns were broken. They are fixed now.
>
> --When "var" was added in 11.3.23, write VAR x "myfile.xxx" broke; that
> is fixed.
>
> --The Jmol Application wasn't allowing multi-line pasting into the
> console. Now it does.
>
> --There was a problem with using atomlist[i] (where atomlist was some
> set of atoms) more than once, as in a for loop, for example:
>
> var theatoms = {model=3}
> var n = theatoms.size;
> for (var i = 1; i <= n; i=i+1);
> print theatoms[i]
> end for;
>
> This should be fixed.
>
>
> Bob
>
>
>
>
>
>
>
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