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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