Thanks a lot for clarifying that Paul! that helped, but I already managed to
pass the value of jmolGetPropertyAsString('stateInfo') in a similar way as
you explain above (almost the same but with post).
I already have the value of jmolGetPropertyAsString('stateInfo') in a php
variable using $_POST["ESTADO"]; the problem I have now is how to make Jmol
understand what is inside that variable... I am trying to implement Bob's
suggestion above with no success... any idea?
Thanks
2011/8/4 Paul Pillot <[email protected]>
> Daniel, I think there is some confusion in your scripts about what is done
> on the client side and what is done on the server side.
> I'll try to explain it :
> - client side you have the Jmol applet embedded in a html page (the html
> code may have been created through php, in the end it's always html from the
> client perspective). The user through javascripts can interact with the web
> page, with the applet and create a view that you may want to save.
> To save the view, you want to interact with the server.
> - server side : you have a php script that receives different requests (for
> example a state script through a form element) and sends an html page (or
> other kind of files/texts,etc...)
>
> So, the first thing you have to decide is when and how your user keeps a
> state of what he is doing. There are several options there. The simplest
> might be to click on a submit button that would trigger your next php page.
> But when the user clicks on submit, you want that the value attached to the
> submit button or to an invisible input element is updated with the value of
> the state script.
> For example, your HTML could look like
> <form method="put">
> <input type="hidden" value="" name="my_script" id="my_hidden_field" />
> <input type="submit" value="Submit !"
>
> onclick="document.getElementById('my_hidden_field').value=jmolGetPropertyAsString('stateInfo')"/>
> </form>
>
> Then in your php you can access to the state script with
> $REQUEST['my_script']
>
> An other option might be to use an ajax library to save the different
> states the user gets on the first page, before loading the next page. I made
> something like that with a kind of snapshot widget that saves states in a
> webpage that could be recalled from an other webpage. If you're interested
> and don't mind french you can have a look at the following link :
> http://librairiedemolecules.education.fr/outils/minuscb/app/minusc.htm If
> you click on "Clichés", you activate that snapshot function. Each "Cliché"
> triggers the saving of a statescript + image in a database, and can be
> accessed from the "export" feature (it's a prototype, I haven't pushed it
> further). In your case, you could save the state script in a php session
> variable to find these back on your subsequent page.
>
> -Paul
>
> Le 4 août 2011 à 15:41, Daniel Carbajo a écrit :
>
> I am trying everything I can think of but does not seem to work... my last
> attempt is the following (saving the jmolGetPropertyAsString("stateInfo")
> output into a file):
>
> In the second php:
>
> $ESTADO=$_POST["ESTADO"];
> echo "$ESTADO";//IT IS SAVED CORRECTLY HERE
> $File = "Jmol-12new/test.sptt";
> $f = fopen($File, 'w') or die("Cannot create file $File");
> fwrite($f, $ESTADO);
> fclose($f);
>
>
> $JMOL = "<script type=\"text/javascript\">
> jmolInitialize(\"Jmol-12new\", true);
> jmolSetAppletColor(\"white\");
> var jmolcmds = [
> \"load $ZIPtoUSE|$PREFIX-Models_$code/$PREFIX-$code.pdb\",
> \"set frank off; select all; hbonds off; spin off; wireframe off;
> spacefill off; trace off; set ambient 40; set specpower 40; slab off;
> ribbons off; cartoons off; label off; monitor off\",
> \"set isosurfacePropertySmoothing TRUE\",
> \"set showAxes true\",
> \"set appendNew true\",
> \"frame all\",
> \"display all\",
> \"select 1.1; cartoon; set propertyColorScheme 'bwr'; color atoms
> property temperature ABSOLUTE $range\",
> \"script Jmol-12new/myJMOLfunctions.spt\",
> \"script Jmol-12new/test.spt\"
> ];
> jmolApplet([580,500], jmolcmds.join(\"; \"));
> jmolScriptWait(\"_setState\");
> </script>";
>
>
> Of course this is NOT working... and I'd rather prefer Bob's way with "Jmol
> Embedded Script" but I really don't know how to make it work... by the
> way, should I keep all the specifications when initializing the applet
> before the state script? Thanks a lot to everyone,
> Daniel
>
>
>
>
>
>
>
>
>
>
> 2011/8/4 Daniel Carbajo <[email protected]>
>
>> OK it seems I am able to pass the jmolGetPropertyAsString("stateInfo")
>> value to a new php doing the following (in case anyone is interested):
>>
>> First php:
>> $cont0 .= "<form name=\"PASARCOLORS\" action=\"MODshowCOLORS.php\"
>> method=\"POST\" onSubmit='var state=jmolGetPropertyAsString(\"stateInfo\");
>> document.PASARCOLORS.ESTADO.value=state;'>";
>> $cont0 .= "<input type=\"hidden\" name=\"ESTADO\"></form>";
>>
>> Second php:
>> $ESTADO=$_POST["ESTADO"];
>> echo "$ESTADO<br>";
>>
>> So now I have it inside a variable in the second php... Should I do
>> something like:
>> $ESTADO="/****Jmol Embedded Script ****".$ESTADO."**/";
>> JmolScript($ESTADO);
>>
>>
>> Besides, answering to Rolf's previous question, the new files I want to
>> load are exactly the same (just the B-factor records change), except for one
>> file, that in the first php contains all chains, and in the second only the
>> chain under study, but with the same coordinates and everything... (hope
>> this is not a problem). In any case I should parse the $ESTADO variable
>> because all pdb file names change, and the labels (though refering to the
>> same residues), are slightly different...
>> Thanks,
>> Daniel
>>
>>
>>
>> 2011/8/4 Daniel Carbajo <[email protected]>
>>
>>> Thanks! I start to understand how this works but I have one problem: I
>>> cannot pass the jmolGetPropertyAsString("stateInfo") information from one
>>> php page to another... I have tried the following with no success:
>>>
>>> First php:
>>> <input type="hidden" name="STATE\"
>>> value='jmolGetPropertyAsString("stateInfo")'>
>>>
>>> Second php:
>>> $STATE=$_POST["STATE"];
>>> echo "$STATE<br>";
>>>
>>> But I get just the command, not the value... So how do you send it to the
>>> new page? I am quite new to all this, sorry. And thanks a lot again!
>>> Yours,
>>> Daniel
>>>
>>>
>>>
>>>
>>>
>>> 2011/8/3 Robert Hanson <[email protected]>
>>>
>>>> Daniel,
>>>>
>>>> Yes, jmolGetPropertyAsString("stateInfo") returns the exact information
>>>> to use to retrieve the exact state. This is what
>>>> http://chemapps.stolaf.edu/jmol/docs/examples-12/JmolPopup.htm uses. If
>>>> it does not reproduce the EXACT state, I want to know. (The only caveat is
>>>> that labels can move if displayed in an applet that has a different size.)
>>>> To use it, just run it with
>>>>
>>>> script [that filename]
>>>>
>>>> or send it to the new page as part of the page (I like to use <--
>>>> /****Jmol Embedded Script **** .... **/ --> comments in the HTML and
>>>> then
>>>> just send the whole page to Jmol with JmolScript (grabbing that with
>>>> document.getElementById(...).innerHTML. That works amazingly well, and you
>>>> don't have to escape anything. The necessary term is
>>>>
>>>> /**** Jmol Embedded Script ****
>>>>
>>>> If Jmol finds that in a file, it reads only the data between that and
>>>>
>>>> **/
>>>>
>>>> and skips everything else in the file.
>>>>
>>>>
>>>>
>>>> On Wed, Aug 3, 2011 at 10:32 AM, Daniel Carbajo <
>>>> [email protected]> wrote:
>>>>
>>>>> The point is that I have a page where I can load many proteins, change
>>>>> them from cartoon to spacefill to whatever, highlight residues in
>>>>> wireframe... and then I have a button which redirects to another page
>>>>> which
>>>>> is similar, but with different proteins, which are actually the same ones
>>>>> but with temperature factor records changed with other descriptors... In
>>>>> this second page I want to restore all the settings from the previous
>>>>> (proteins loaded, whether they are in cartoon, spacefill, etc., residues
>>>>> highlighted, orientation...).
>>>>> Which do you think would be the best way to do so?
>>>>> Does jmolGetPropertyAsString("stateInfo") return all that information?
>>>>> If so, I am not so sure where to put it so it can be used by the second
>>>>> page...
>>>>> This is my first attempt in php:
>>>>> $content .= "<form><button type=\"submit\" onClick='var
>>>>> state=jmolGetPropertyAsString(\"stateInfo\");
>>>>> alert(state)'>CHECK</button></form>";
>>>>> But I do not want a button and an alert... besides the output is cut so
>>>>> I do not get to see everything that jmolGetPropertyAsString("stateInfo")
>>>>> returns... Any suggestions?
>>>>> Thanks again,
>>>>> Daniel
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> 2011/8/3 Rolf Huehne <[email protected]>
>>>>>
>>>>>> On 08/03/2011 03:04 PM, Daniel Carbajo wrote:
>>>>>> > Hello everyone,
>>>>>> > is it possible to save a Jmol session in terms of proteins loaded,
>>>>>> their
>>>>>> > displays (cartoon, spacefill...), residues selected, labels, etc. in
>>>>>> one php
>>>>>> > page so everything is restored in another? Can I save the session
>>>>>> > specifications into a file that is read by another php page? I am
>>>>>> trying
>>>>>> > with save/restore ORIENTATION saveName, but does not seem to be
>>>>>> working.
>>>>>> The "save state" command does this.
>>>>>> (see
>>>>>>
>>>>>> http://jena3d.fli-leibniz.de/ImgLibPDB/Jena3D/doc/jmol_scripting/index.htm#save
>>>>>> )
>>>>>>
>>>>>> But you will need the "signed" Jmol applet to be able to write it
>>>>>> directly into a file.
>>>>>>
>>>>>> With the "unsigned" Jmol applet you can open the Jmol console, display
>>>>>> the state (by clicking on a button) and copy+paste the state into a
>>>>>> text
>>>>>> editor and save it into a file.
>>>>>> But depending on the combination of Java, browser and operating system
>>>>>> version there might be copy+paste problems.
>>>>>>
>>>>>> With both applet types you could read the state information with
>>>>>> javascript and then send the data to a server for storage:
>>>>>>
>>>>>> state = jmolGetPropertyAsString("stateInfo");
>>>>>>
>>>>>> Depending on the location of the other PHP page and the directory
>>>>>> organization at this site it might be becessary to adapt the state
>>>>>> script to the new location before it is loaded properly.
>>>>>>
>>>>>> Regards,
>>>>>> Rolf
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> BlackBerry® DevCon Americas, Oct. 18-20, San Francisco, CA
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>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
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>>>>>
>>>>
>>>>
>>>> --
>>>> Robert M. Hanson
>>>> Professor of Chemistry
>>>> St. Olaf College
>>>> 1520 St. Olaf Ave.
>>>> Northfield, MN 55057
>>>> http://www.stolaf.edu/people/hansonr
>>>> phone: 507-786-3107
>>>>
>>>>
>>>> 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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>>>
>>
>
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