Hi again,
Currently, the extension needs to use the signed applet when working with
the SMILES string or the PDB code.
That's normal because it requires services hosted by other sites, but it's
not very user friendly.
I'd like to be able to use the unsigned applet even for SMILES string or PDB
code.
I was thinking of configuring Apache on the server hosting the wiki so that
a local URL is redirected to the correct URL.
What are the exact URL used for SMILES and PDB ?
Is it possible to configure Jmol for using a different URL than the default
for resolving a SMILES string (other than cactus.nci.nih.gov) or a PDB code
(other than www.rcsb.org) ?
That way, the syntax will still be the same in Jmol script (load $SMILES or
load =PDB) but the call will go through the wiki server.
Nico
On Sun, Nov 28, 2010 at 11:39 PM, Nicolas Vervelle <[email protected]>wrote:
> Hi,
>
> The Jmol extension now has simple tags for loading molecules directly with
> a SMILES string or a PDB code.
> Examples are available at
> http://wiki.jmol.org/index.php/MediaWiki/Basic_Example
>
> Nico
>
> 2010/11/23 Angel Herráez <[email protected]>
>
> Nico,
>>
>> > Can Jmol show a molecule having just a SMILES string ?
>>
>> Yes, Jmol can do it, but
>> 1. it relies on an external server being available (it does the
>> calculation from smiles to 3D)
>> 2. we need the signed applet for that (which is a concern for WP, since
>> the Java security
>> warning to load the signed applet may deter users)
>>
>> > If so, what are the commands that need to be executed ?
>>
>> load "$CCCNC"
>> /the quotes may be omiited is the string is not conflictive)
>>
>>
>> > I think we could add a syntax for Wikipedia where a user would simply
>> have to add something like
>> > <smiles>XXXX</smiles> todisplay the molecule in Jmol.
>>
>> Maybe, to display a link that will open a popup or insert a DIV with Jmol
>>
>>
>> > Also, can Jmol retrieve a molecular file using only an identifier (like
>> getting the molecule on the
>> > pdbdatabase) ?
>>
>> Again, yes. From the PDB server using the PDB 4-character ID.
>> Same concerns: signed applet, external server.
>> Syntax is
>>
>> load "=1CRN"
>>
>>
>>
>>
>>
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