On Tue, Mar 18, 2014 at 2:48 PM, tinus updates <tinusupda...@gmail.com>wrote:
> Thank you all!
>
> I have understood that Jmol.getTMApplet uses JSmol.lite.js or
> JSmol.lite.nojq.js. So I adapted the lite4.htm file provided in the
> distribution. The other liteX.htm files did not work "out of the box", so I
> left them aside.
>
> yes, I just spotted that bug. It has to do with reading files from
PubChem.
> Robert, I found your quoted code in js/JSmol.full.lite.js and
> js/JSmol.full.lite.nojq.js and js/JSmolTM.js, but not in JSmol.lite.js. Now
> I'm somewhat confused on which JSmolXXX.js I should use best for viewing
> PDB on iPads, and if JSmol.lite(.nojq).js does (as the other files) support
> just MOL at the time.
>
JSmol.full.lite.nojq.js is just the uncompressed version of
JSmol.lite.nojq.js -- no need to use that except for debugging. Same for
JSmol.full.lite.js and JSmol.lite.js, and JSmol.full.js and JSmol.min.js.
JSmol.lite.js is light, but also contains jQuery, which you need. So if you
are not already using jQuery, use that. The nojq.js version is for
developers who need to use or want to use their own version of jQuery --
usually in larger sites such as RCSB. That one is super-light (51K).
>
> The xyz.gz file at www.permafrost.ch/jsmol/eis-lite.htm was a left-over
> from testing, it is now replaced with the correct sz/ice.pdb.
> I wonder by the way if a bigger molecule or structure is displayed clearly
> enough with the limited rendering.
>
>
Once again, you must use MOL file format for JSmol-Lite. Just read that
file into any other version of Jmol and then use
select *
write "eis.mol"
to create the MOL file version. You are under 1000 atoms, so that should be
fine.
Bob
>
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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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"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/13534_NeoTech
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