> > RasMol commands return useful information e.g.
> > select HIS
> > returns something like 8 residues selected,
>
> So, this information is displayed for the user to read, but the results
> are never actually interpreted by any tools or external program ...
> correct?
>
I tried with RasMol the command "select HIS" and it only returns the number
of selected atoms, not the number of residues. It's the same with Chime.
If I type "show selected", in RasMol (v2.7.1), the list of the selected
atoms with their respective chains and residues is displayed.
In Chime, the same command only hilights the selected residue in orange in
the visualisation frame.
To get the name of selected resiudes with Chime the command is "show
residue"
To get the numbers of selected atoms, the command is "show atom", and for
the selected chains "show chain"
These commands are Chime specific
With Chime, as these informations are sent to a javascript function, they
can be interpreted to perform some operations such as : actualisation of a
counter, selection of residue (the non covalent bond finder from Eric Martz,
use these informations a lot), selction of a chain (for example in MolUSc to
color RNA in a different color than DNA, I use the following selection
"select nucleic and *.o2*; show chain" and I use the information from "show
chain to select only the RNA)
> So the actual format of the output does not need to be RasMol/Chime
> compatible ... correct?
It's a tricky question...
An array is very interesting to get some messages that need to be
preformated. But for some other messages one string is sufficient (the
command executed, the result of "show view").
It will break compatibility with existing web pages, but in fact pages which
use these informations are not common and will benefit from these changes.
What do you think about receiving these informations as a fourth argument
from the messageCallBack method ?
- 1st : applet name
- 2nd : string
- 3rd : number of the message
- 4th : array if needed
So, when some informations come in an array, the 2nd argument could "tell
it"
(as I was writing this message, I received a message from Miguel speaking of
a fourth argument too)
> Is 'show selected residues' an existing RasMol/Chime command or a 'new'
> command?
It's an existing Chime command
> > I hope we don't need an extra dummy frame:-)
>
> I assume that the 'extra dummy frame' is related to some quirk in Chime
> web app development ... what is it?
Netscape Communicator can interact directly from javascript with Chime using
LiveConnect, with the execute script method. So to send a command to chime
with javascrip, in Communicator you can use
document.chimePluginName.executescript("the commands of the script"); Before
this method was available, the only way to interact with Chime was with
buttons. In this page, when you type in a command and execute it, an
invisible button is written in an invisible frame at the bottom of the page.
This method is the only one to work with Internet Explorer and Mozilla.
It's mot usefull with Jmol
Paul
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