On Wed, Feb 24, 2010 at 3:24 PM, Otis Rothenberger <o...@chemagic.com>wrote:
> I included point and click atom and bond deletion into a Jmol molecular
> editor. This works just fine, but there are some deletion followup issues:
>
> 1) minimize addHydrogens is not functional on a multivalent atom that has
> atoms deleted or bonds broken.
>
Hmm. Thought I fixed that. You sure? I do this:
load caffeine.xyz
set picking deleteatom
[click on the NH hydrogen, and it disappears]
minimize addHydrogens
[two H atoms appear on that N, which is correct, since I don't have multiple
bonding in this model, and the model minimizes]
I do this:
load caffeine.xyz
connect {N21} {c20} double
set picking deleteatom
minimize addHydrogens
[one H appears on that hydrogen, and the minimization looks good.]
So what am I missing?
3) The exception: If the multivalent atom is not connected to any other
multivalent or non-hydrogen atoms, then the atom replacement step above
simply creates a single atom with no hydrogen atoms attached.
That I believe. An atom by itself with no connections will not generate a
full set of H atoms. We could program Jmol to do that, just haven't.
Bob
>
> By way of example, if I break a C-C bond in cyclohexane, then the terminal
> CH2 groups will be rectified by the following swap - i.e. both end C's are
> swapped with new C's:
>
> evalRasmol("{atomIndex = _atomPicked}.element = '" + buildAtom +
> "';");
> evalRasmol("select hydrogen and connected({atomIndex =
> _atomPicked});delete selected;");
> evalRasmol("minimize addHydrogens;");
> evalRasmol("select *;wireframe 0.15; spacefill 23%;boundbox
> {*};centerat boundbox;echo Calculating UFF Minimum...;");
> evalRasmol("minimize steps 100;");
>
>
I really need to see the Jmol script, not this. Perhaps displaying the
command history. Also, I'm wondering why you want to do all those individual
scripts. Why not just one:
jmolScript("{atomIndex = _atomPicked}.element = '" + buildAtom
+ "';select hydrogen and connected({atomIndex =
_atomPicked});delete selected;"
+ "minimize addHydrogens;select *;wireframe 0.15; spacefill
23%;boundbox {*};centerat boundbox;echo Calculating UFF Minimum...;minimize
steps 100;");
Hmm, now looking at that -- Why two minimize commands?
When I do this, I'm really using jmol.js and the jmolScript() function. By
> running this script text through a function of my own before jmolScript(), I
> have the ability to define some jmol script commnads of my own from
> jmolScript combinations. I'm not suing any of my defined commands above.
>
>
sure - wish you wouldn't call it "evalRasmol" though. Not much "Rasmol" in
it! :)
> Continuing with my example, if I break a methly group off of hexane with
> the intent of reconnecting the pieces to form 2-methylpentane, then all is
> well. But if I try to rectify the fragments by the swap described above to
> create a molecule of methane and a molecule of pentane, then pentane forms,
> but the CH3 fragment is reduced to a single carbon atom that cannot be H
> rectified.
>
>
right -- haven't implemented adding a full set of H atoms to a C.
> As a point of information, if I break hexane into two CH3CH2CH2 fragments,
> I can reconnect the two fragments any way I want. I can also make two
> separate molecules of ethane. It appears that breaking off the following
> groups from a larger molecule creates the problem described above:
>
> CH3
> OH
> NH2
> SH
>
> Any suggestions?
>
>
Once the C is reconnected, it sprouts 3 H atoms, right?
Bob
> 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
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
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
------------------------------------------------------------------------------
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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
