curiously, that's supposed to read:
load /*file*/ inline
That's the real problem. I wonder why that is not there?
On Sat, Mar 1, 2014 at 7:54 AM, Otis Rothenberger <[email protected]>wrote:
> Angel,
>
> When I run this with cyclopropane, there appears to be a *ZAP* in the
> state script before the H atom append that is causing the problem. See
> below:
>
> load inline "C1CC1\nJME 2013-10-12 Sat Mar 01 08:49:47 GMT-500 2014\n
> \n 3 3 0 0 0 0 0 0 0 0999 V2000\n 1.4000 0.0000 0.0000
> C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.7000 1.2124 0.0000
> C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000
> C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 1 0 0 0 0\n 2 3 1 0
> 0 0 0\n 3 1 1 0 0 0 0\nM END\n";
> *zap*;load /*data*/ data "append inline"
> 6
> Viewer.AddHydrogens#noautobond
> H 1.8162266141787846 -0.240300337429973 1.28944992469569 - - - - 4
> H 2.1677857734265977 -0.44327906678783263 -0.3511594851274376 - - - - 5
> H 0.8803091480224934 1.8098881118508672 -0.9058126557607197 - - - - 6
> H 0.5287499887746805 2.012866841208727 0.7347967540624076 - - - - 7
> H -0.4272906203972308 -0.45489682342005144 -0.9058099170150967 - - - - 8
> H -0.7788497796450441 -0.2519180940621916 0.7347994928080308 - - - - 9
> end "append inline";;
>
>
> Otis
> --
> Otis Rothenberger
> [email protected]
> http://chemagic.com
>
>
> On Mar 1, 2014, at 7:15 AM, Angel Herráez <[email protected]> wrote:
>
> Hello
>
> I have a tricky issue in saving and retrieving the state after the model
> has
> been modified by
> calculate hydrogens; minimize;
> or
> minimize addHydrogens;
>
> Summary:
> Running the state as a script brings a model with all hydrogens and some
> other atoms also as hydrogens (but not all); other atoms are lost.
>
> This is in JSmol 14.0.10 (meant to be put in an "open this model in a big
> window), but the generated state is wrong even when applied to Jmol app.
> The model does not come from file but from a structure drawn in JSME.
>
> Procedure is:
> 1. draw a structure in JSME
> 2. transfer it as molFile
> 3. add hydrogens and minimize
> 4. get the state
> 5. apply the state to another instance of JSmol --or to the Jmol app
>
> It is step #3 that creates the problem and, specifically, the addition of
> Hs
>
> If I transfer as JME string rather than molFile data, the problem seems to
> be
> also there (since Hs are being added internally by Jmol).
> No problem when I transfer as Smiles
>
> Test case: go to
> http://biomodel.uah.es/en/DIY/JSME/
> (that uses 14.1.8, but the problem is the same)
>
> Draw something, transfer as MOL, open JSmol console and
> show state
> copy it and paste back into the consle or Jmol app's console
> JME transfer is working fine in that page; I must find out what's the
> difference
> with my current page -- But I really want to use MOL transfer
>
> Thanks
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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