Jalview applet issue

Hi Jeanre,

I've copied your mail and my reply to the jalview-discuss mailing list
as then the others (who are probably more competent than me to answer
your queries) will see it.

As far as I can tell there isn't a way to explicitly load a structure
into Jalview from the command line or an applet parameter. Your
immediate best options might be to try a groovy script that would call
the relevant menu options.

This is not particularly well documented yet.

..d

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College of Life Sciences
University of Dundee
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On 18/03/2011 at 09:31, in message <AANLkTikfq0iCWapf5i-m3dK8dT5Zcfw_TKsiW_t0SnjG@mail.gmail.com>, Jeanré Smit<jeanre.smit@gmail.com> wrote:

Hello this is Jeanre from the University of Pretoria. We are now
implementing Jalview to view sequences and associate PDB files with
those sequences. I was wondering if there was a way to pass a STRING
of a PDB file, instead of that file's filename, to the applet

version

of Jalview. As far as I could tell there isn't. If there isn't, is
there a way for me to add such functionality to the jalview.jar that
I'm currently using? (It would probably have to be rebuilt.)

Thank you in advance.

The University of Dundee is a registered Scottish charity, No: SC015096

Hi David, Jeanre - apologies - I spoke to david, but didn't actually
post an answer here.

As far as I can tell there isn't a way to explicitly load a structure
into Jalview from the command line or an applet parameter. Your
immediate best options might be to try a groovy script that would call
the relevant menu options.

There are parameters for loading structures into the applet - there's
even an example here: http://www.jalview.org/examples/applets.html (the
third applet button opens an alignment with a structure associated). But
as Jeanre points out - they only take URIs that resolve to the PDB file
data, rather than allowing one to paste the contents of a PDB file directly.

<AANLkTikfq0iCWapf5i-m3dK8dT5Zcfw_TKsiW_t0SnjG@mail.gmail.com>, Jeanré

> Hello this is Jeanre from the University of Pretoria. We are now
> implementing Jalview to view sequences and associate PDB files with
> those sequences. I was wondering if there was a way to pass a STRING
> of a PDB file, instead of that file's filename, to the applet

There is a javascript accessible method in the development version of
the applet that lets you add a PDB file association directly (with PDB
data provided directly or specified as URL), but I haven't as yet
implemented an applet parameter that allows you to do something like :
<param name="PDBFile1" value="FER1_SPIOL paste:HEADER
OXIDOREDUCTASE/ELECTRON TRANSPORT 08-MAY-00 1GAQ
ATOM 2 CA GLU A 19 20.491 30.713 36.290 1.00
74.29 C
ATOM 11 CA SER A 20 24.056 29.774 37.264 1.00
72.09 C
ATOM 17 CA LYS A 21 27.517 31.289 37.563 1.00
70.09 C
ATOM 26 CA LYS A 22 28.794 27.865 36.481 1.00
68.64 C
ATOM 35 CA GLN A 23 29.484 26.806 32.884 1.00
70.46 C
ATOM 44 CA GLU A 24 26.420 25.175 31.360 1.00
72.08 C
ATOM 53 CA GLU A 25 26.736 26.049 27.683 1.00
70.43 C
..
">

> of Jalview. As far as I could tell there isn't. If there isn't, is
> there a way for me to add such functionality to the jalview.jar that
> I'm currently using? (It would probably have to be rebuilt.)

It certainly would involve it having to be recompiled - and you're very
welcome to do so!
if you are a Java programmer then feel free to take a look at the
applet's code - its all available for download at
www.jalview.org/source.html

I've also opened up a feature request on the Jalview issues tracker :
http://issues.jalview.org/browse/JAL-803

Jim.

···

On 18/03/2011 09:46, David Martin wrote:

Smit<jeanre.smit@gmail.com> wrote:

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