Luciano,
A "show ThisStuff" command is really an instruction to send ThisSuff to
the Message Call back function if it exists, so show sequence will work for
you as well as show residues.
Since you are new to the JSmol call back approach for grabbing a variable,
give me about 15 minutes to put together an example of how you could put
the sequence or residues into a JavaScript variable.
Back to you in about 15 minutes...
Otis
----------------------------------------
From: "Luciano Abriata" <luciano_abri...@yahoo.com>
Sent: Sunday, January 18, 2015 1:19 PM
To: "jmol-users@lists.sourceforge.net" <jmol-users@lists.sourceforge.net>
Subject: Re: [Jmol-users] JSmol: how to put a protein's sequence into a
javascript variable
Hi Otis,
Thanks for your help and time. I'm not sure if my question was clear
enough, or if it was but I am not understanding your answer.
What I want to do is the following. I have a working JSmol applet, with a
PDB file loaded. Then I have a piece of javascript code doing stuff, and at
some point I want something like
...
var protein_sequence = (something here that retrieves the protein's
sequence from the running JSmol)
...
That said, it is totally unclear to me where the "show SEQUENCE" would go
(in a function for the messagecallback?), whether I need to set up anything
like Info.messagecallback at all, and where will I get the "waves" of data
that include the sequence... In brief, I have no clue!
Thanks again!
Luciano
----------------------------------------
De: Otis Rothenberger <osrot...@chemagic.com>
Para: Luciano Abriata <luciano_abri...@yahoo.com>;
"jmol-users@lists.sourceforge.net" <jmol-users@lists.sourceforge.net>
Enviado: Domingo, 18 de enero, 2015 17:56:42
Asunto: Re: [Jmol-users] JSmol: how to put a protein's sequence into a
javascript variable
Hi Luciano,
Bob may have a more elegant solution to your problem, but I am interested
in your question because I guess I learned something about SHOW and PRINT -
i.e. they are not synonymous. I thought a simple
Jmol.evaluate(jmolApplet0,"show residues" would work - not so. When I
checked the docs, they clearly say that this command works with anything
that works with the PRINT command (NOT the SHOW command), and "show
residues" and "print residues" do not both result in residues! So unless
I'm mistaken, you have to get this with a message callback function.
If you set up a message callback function of the form:
function MyCallBack(X, Y, Z) {
Do Stuff Based ON X, Y, Z
}
The " " will produce three waves of XYZ activity (my applet below is
jmolApplet0):
WAVE 1
X=jmolApplet0
Y=script 13 started
Z=show residues## EDITOR_IGNORE ##
WAVE 2
X=jmolApplet0
Y=[PCA]1:A
[TYR]2:A
[SER]3:A
... Long list of residues (Your Stuff!)
Z=1
WAVE 3
X=jmolApplet0
Y=Script completed
Z=EMPTY}
In MyCallBack, you have to use WAVE1 as a heads up to grab Your Stuff in
WAVE2.
Otis
On Sat, Jan 17, 2015 at 1:30 PM, Luciano Abriata
<luciano_abri...@yahoo.com> wrote:
Hello!
I need to get the contents of "show RESIDUES" or "show SEQUENCE" from a
PDB file loaded in JSmol, and put that into a javascript variable so as to
play with it afterwards.
I tried many things with no success, maybe because I don't understand how
message callbacks and such work. I'm now totally lost!
Can anybody help me out?
Thanks,
Luciano
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