Hello-
I'm working on an atom append script to click append a C atom (methyl group
actually) to an existing atom in a Jmol model. The following JavaScript
function works, but it is far from elegant. I'm fairly sure that there are
Jmol math approaches to deal with some specific script actions that I'm
attempting, but I could use some guidance. I'm new to Jmol math. The
function and my questions:
function appendC(x) {
var scpt = "select;set appendNew false;data 'append'|1|add|At 2 2 2|end
'append';show data;select astatine;"
scpt += "{selected}.element='C';connect (selected)(atomIndex=" + x +
");select *;wireframe 0.15; spacefill 23%;boundbox {*};"
scpt += "centerat boundbox;delete hydrogens;minimize addHydrogens;"
jmolScript(scpt, "01");
}
x is the atomIndex of the clicked atom via a pickCallback function.
1) The ridiculous addition of astatine relates to my inability to use
getProperty for the atomIndex of the newly appended atom, so I appended a
very rare element, selected it, and changed it to carbon. Is there a way to
get this atomIndex a bit more gracefully?
2) The 2 2 2 coordinates were selected to get the appended atom away from
existing atoms in ammonia. I'd really like a general approach to get this
atom outside of the VDW surface of any molecule. I know how to calculate the
isosurface area if I generate it, but I really don't want a surface painted
on the screen. Further, I'm not sure the area will help. I could calculate a
diameter, but in a long molecule, I would still be in trouble. Is there any
Jmol math approach that will calculate a safe distance for this appended
atom?
3) One approach is to really put the appended atom into orbit. The
coordinates 50 50 50 actually work with ammonia. By using a zoom 2000, you
can even see the result. The function really works very nicely if you get
the appended atom away from existing atoms. If you do not, then the minimize
produces chemical nonsense even though I explicitly connect only the two
atoms. If this orbit approach turns out to be the best approach, then a
scaling factor that normalizes molecule size would be useful. One
possibility is using math with zoom 100 and the orbit coordinates, 50 50 50.
Is this math doable with zoom? Is there another math approach that can be
used to redefine zoom 100?
Any help with the above questions would be appreciated.
Otis
--
Otis Rothenberger
http://chemagic.org
------------------------------------------------------------------------------
Download Intel® Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
