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
o...@chemagic.com
http://chemagic.com
On Mar 1, 2014, at 7:15 AM, Angel Herráez <angel.herr...@uah.es> 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
>
>
>
> ------------------------------------------------------------------------------
> Flow-based real-time traffic analytics software. Cisco certified tool.
> Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
> Customize your own dashboards, set traffic alerts and generate reports.
> Network behavioral analysis & security monitoring. All-in-one tool.
> http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
------------------------------------------------------------------------------
Flow-based real-time traffic analytics software. Cisco certified tool.
Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer
Customize your own dashboards, set traffic alerts and generate reports.
Network behavioral analysis & security monitoring. All-in-one tool.
http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
