jmol-14.1.11_2014.03.01.zip
On Sat, Mar 1, 2014 at 5:20 PM, Robert Hanson <[email protected]> wrote:
> 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
>
>
--
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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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.
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