Hey there, Congratulation Gilleain! This is it! ;) I am sorry for the lack of explanation about CNS. Actually, I just wanted to specify that the structure is generated via an external program. CNS aims at determining the structure of macromolecules from a wide range of (experimental) restraints. Hence, with CNS, you can perform molecular simulation dynamics and minimization of biological systems. More roughly, you can estimate the behaviour of a biological system.
Actually, David, you are right. I can always transform the pdb file which is generated by CNS and create a "JmolInLine readable" file. But I guess this becomes very tricky. I believe that creating a pdb file with a random name and deleting it once it is not requiered anymore would save time and memory. Thanks a lot a again for your help. :D Cheers, Mickael On Fri, 19 Jun 2009, gilleain torrance 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 > > >> > > > >> > > > >> > > > ------------------------------------------------------------------------------ > > >> > Crystal Reports - New Free Runtime and 30 Day Trial > > >> > Check out the new simplified licensing option that enables unlimited > > >> > royalty-free distribution of the report engine for externally facing > > >> > server and web deployment. > > >> > http://p.sf.net/sfu/businessobjects > > >> > _______________________________________________ > > >> > Jmol-users mailing list > > >> > [email protected] > > >> > https://lists.sourceforge.net/lists/listinfo/jmol-users > > >> > > > >> > > >> > > ------------------------------------------------------------------------------ > > >> Crystal Reports - New Free Runtime and 30 Day Trial > > >> Check out the new simplified licensing option that enables unlimited > > >> royalty-free distribution of the report engine for externally facing > > >> server and web deployment. > > >> http://p.sf.net/sfu/businessobjects > > >> _______________________________________________ > > >> Jmol-users mailing list > > >> [email protected] > > >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > >> > > > > > > > > ------------------------------------------------------------------------------ > > > Crystal Reports - New Free Runtime and 30 Day Trial > > > Check out the new simplified licensing option that enables unlimited > > > royalty-free distribution of the report engine for externally facing > > > server and web deployment. > > > http://p.sf.net/sfu/businessobjects > > > _______________________________________________ > > > Jmol-users mailing list > > > [email protected] > > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > > > > > ------------------------------------------------------------------------------ > > Crystal Reports - New Free Runtime and 30 Day Trial > > Check out the new simplified licensing option that enables unlimited > > royalty-free distribution of the report engine for externally facing > > server and web deployment. > > http://p.sf.net/sfu/businessobjects > > _______________________________________________ > > Jmol-users mailing list > > [email protected] > > https://lists.sourceforge.net/lists/listinfo/jmol-users > > > ------------------------------------------------------------------------------ Crystal Reports - New Free Runtime and 30 Day Trial Check out the new simplified licensing option that enables unlimited royalty-free distribution of the report engine for externally facing server and web deployment. http://p.sf.net/sfu/businessobjects _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
