however the PHP creates the file, it has access to the file contents as well
as the name itself. I'm just suggesting you send the file contents rather
than the name.
On Fri, Jun 19, 2009 at 6:48 AM, gilleain torrance <
[email protected]> wrote:
> Well, the 6th hit on google (after the Catholic News Service, and the
> Congress of Neurological Surgeons) is:
> http://cns-online.org
>
> which is the crystallography and NMR system. I'm guessing that's it?
>
> gilleain
>
>
> On Fri, Jun 19, 2009 at 11:56 AM, N David Brown <[email protected]>wrote:
>
>> I've no ideas what CNS stands for, and Google simply comes up with
>> many 'Central Nervous System' links! You'll have to see whether you
>> can change the output of CNS to be something other than a file, e.g. a
>> stream on a socket which you can read directly via PHP. If you can't,
>> you'll just have to wait until CNS has generated the molecule in a
>> file, then delete it when the PHP reads it in and transmits it to a
>> user, upon request.
>>
>> - N David Brown
>>
>>
>>
>> 2009/6/19 Mickael Krzeminski <[email protected]>:
>> > Hi everyone,
>> >
>> > You gave me very nice remarks! Thanks a lot for taking time with my long
>> > explanation.
>> > In the meantime, I tried the idea of creating the name of the molecule
>> > with a random string (molecule8ruO.pdb, moleculehJ23ER.pdb,...) and it
>> > works. But, I do like a lot this idea about this Inline mode, which
>> would
>> > make me save time and memory space actually.
>> >
>> > But, the molecule is not generated by the PHP program, but an external
>> > program (CNS). In other word, the php page make use of "system" to
>> > generate the structure with CNS. The output of such a program looks more
>> > like a logfile, not a structure file. The only way to get your structure
>> > consists of writing it in the CNS script.
>> >
>> > Any clue ?
>> >
>> > Thanks again,
>> > Mickael
>> >
>> >
>> > On Fri, 19 Jun 2009, Mickael Krzeminski wrote:
>> >
>> >> Hey there,
>> >>
>> >> Thanks a lot for all you comments and remarks. I'm gonna explain somme
>> >> more details.
>> >> Actually, I'm using AJAX to call the php file, which will generate the
>> >> molecule and display it (More or less in the way you, David,
>> described).
>> >> In this script, I put a listbox from which the user can select
>> different
>> >> molecules. Once selected, the user can visualize it by clicking a
>> button,
>> >> which calls something like disp_mol.php?name=arginine. The php file
>> will
>> >> parse it to retrieve the name of the molecule, generate it, and call it
>> >> molecule.pdb (no matter the name of the molecule). Then, it loads
>> >> molecule.pdb into Jmol.
>> >>
>> >> As you probably understood, each molecule is not present on the server,
>> >> but is generated only when the user presses the button (I'm not gonna
>> give
>> >> the reason for this because of too many details... ;) )
>> >> At this time, a new directory is created on the server (This helps me
>> >> keep some traces and is easier to handle). The name of the directory is
>> >> unique for each user (It is based on the IP). When a molecule is
>> >> generated, it is stored in this directory. Hence, if I manually delete
>> >> this directory, no molecule is present anymore.
>> >> So, on the webpage, I clicked the button to display the molecule A and
>> it
>> >> appeared correcly. Then, I deleted the directory that was created. I
>> >> restarted the same webpage after erasing all Internet traces (I also
>> >> thought about a cache problem). I selected another molecule (B) to
>> display
>> >> and... A appeared!!
>> >> Nevertheless, when I asked for viewing the molecule, B appeared (I
>> tried
>> >> under PyMol and MDL). This means that Jmol loaded well the structure,
>> >> right ? The problem could come, as you, Angel and Robert, suggested,
>> from
>> >> Java cache.
>> >> But, do you have any clue about how to flush it from php (or something
>> >> else, without making the user manually intervene) ?
>> >>
>> >> Besdies this, David, the method you propose is clever and easy to set,
>> but
>> >> this can become quite heavy, in particular with large molecule. In that
>> >> sense, I'm not sure this approach would be the most efficient.
>> >> I'm gonna try to add a random code after the name of the molecule to
>> >> download to see the result and will let you know!
>> >>
>> >> Thanks again.
>> >>
>> >> Mickael
>> >>
>> >>
>> >>
>> >> On Thu, 18 Jun 2009, Mickael Krzeminski wrote:
>> >>
>> >> > Dear Jmol users,
>> >> >
>> >> > I recently met a problem when displaying a structure, which does not
>> >> > correspond to the one I loaded.
>> >> >
>> >> > To be clearer... I created a webpage, which displays several buttons,
>> >> > which correspond to different molecules.
>> >> > Every time you click on a button, the information is sent to the
>> >> > server, which generates the structure and creates the corresponding
>> pdb
>> >> > file. Then, a window opens and initialises Jmol before reading and
>> >> > displaying the structure. The structure has always the same name, but
>> the
>> >> > contents of the file is obviously different.
>> >> > The problem there is that the structure is always the same! But...
>> >> >
>> >> > 0. Let us call A the structure that is always displayed and B the one
>> I
>> >> > want to see.
>> >> > 1. I checked out directly the file on the server and the generated
>> pdb
>> >> > structure is well B, even though the one which is displayed is A.
>> >> > 2. The structure A does NOT exist at all on the server (Because it
>> has
>> >> > never been generated). How Jmol can still find it ?
>> >> > 2. With the dropdown menu of Jmol, I asked for downloading the file.
>> And
>> >> > when I open this file locally (With PyMol for instance), I get the
>> correct
>> >> > structure, B.
>> >> >
>> >> > Any clue ? Thanks a lot for all your remarks and comments.
>> >> >
>> >> > Cheers,
>> >> > Mickael
>> >> >
>> >> >
>> >> >
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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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