[Jmol-users] Jmol read/write rights
Hi I have posted questions previously about read/write rights with Jmol. I have the following setup: We run a signed Jmol in Tomcat from a *nix server. Currently the user can upload a PDB file to be viewed. This PDB file is written to /tmp/test.pdb on the server. I then want Jmol to read /tmp/test.pdb but this is not happening. I thought the signing of the applet would help but then realised that this is only only applicable on the client machine and not the server. What is the reason why Jmol cannot read the /tmp/test.pdb file (started with the command jmolApplet(500, load /tmp/test.pdb) )? Does it have to do with read/write permissions imposed by Tomcat? Any simple solution for solving this? I also don't want to store the files inside the Jmol launch directory. Previously some suggestions was to load the file as a url but this would require Apache rule rewrites and I want to avoid going that way if possible... Any suggestions would be more than welcome! -- Tjaart de Beer - The software required Windows XP or better ... so I installed Linux --- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnkkid=110944bid=241720dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Re: Loading an pdb file from a url
Hi I have investigated the different options proposed by everyone with reagrds to enabling a user to load a file into Jmol from a webpage and are leaning towards the signed applet way. I am also investigating wheterJavascript can take Java objects as arguments in a JSP. If this works then I can just write a Java class to retrieve the file from the PDB and post it as an object to the JSP page which hosts Jmol (or as a Stream object). I will keep everyone updated as to the progress. Any suggestions are always welcome! -- Tjaart de Beer Bioinformatics and Computational Biology Unit Department Biochemistry FABI Square/Bioinformatics building Faculty of Natural Sciences University of Pretoria Lynwood rd Pretoria South Africa 0001 Tel:+27 12 420 5802 Cell: +27 83 504 7914 Fax:+27 12 420 5800 Email: [EMAIL PROTECTED] [EMAIL PROTECTED] - The software required Windows XP or better ... so I installed Linux --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://sel.as-us.falkag.net/sel?cmd=lnkkid=103432bid=230486dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Loading an pdb file from a url
Hi I am a newbie tryinh to developing pages with javascript. I am trying to enable a user to load any pdb file (from the PDB) into Jmol from a webpage. I have tried using the following: jmolApplet(600, load http://www.pdb.org/pdb/files/1tx2.pdb;); without any success. It gives me an error saying bad URL but if I open up the link in Firefox I see the physical pdb file. The idea is to allow the user to type in a pdb file code which will then be automatically loaded. Any ideas? Thanks for any suggestions! -- Tjaart de Beer University of Pretoria Lynwood rd Pretoria South Africa 0001 Email: [EMAIL PROTECTED] [EMAIL PROTECTED] - The software required Windows XP or better ... so I installed Linux --- This SF.net email is sponsored by: Splunk Inc. Do you grep through log files for problems? Stop! Download the new AJAX search engine that makes searching your log files as easy as surfing the web. DOWNLOAD SPLUNK! http://ads.osdn.com/?ad_id=7637alloc_id=16865op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Embedding Jmol Solution
Hi Miguel Thanks for the tips on embedding Jmol. I misunderstood the meaning of the jmolInitialize(../../jmol) command. I thought it referred to the executable itself and not to the directory (seeing as they have the same name...). It now works in plain HTML as well as a .jsp page. Thanks again!! -- Tjaart de Beer Bioinformatics and Computational Biology Unit Department Biochemistry FABI Square/Bioinformatics building Faculty of Natural Sciences University of Pretoria Lynwood rd Pretoria South Africa 0001 Tel:+27 12 420 5802 Cell: +27 83 504 7914 Fax:+27 12 420 5800 Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] - The software required Windows XP or better ... so I installed Linux --- This SF.Net email is sponsored by: NEC IT Guy Games. How far can you shotput a projector? How fast can you ride your desk chair down the office luge track? If you want to score the big prize, get to know the little guy. Play to win an NEC 61 plasma display: http://www.necitguy.com/?r=20 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol documentation
Hi Are the Jmol documentation available as PDF (the scripting as well as the development docs)? Thanks!! -- Tjaart de Beer Bioinformatics and Computational Biology Unit Department Biochemistry FABI Square/Bioinformatics building Faculty of Natural Sciences University of Pretoria Lynwood rd Pretoria South Africa 0001 Tel:+27 12 420 5802 Cell: +27 83 504 7914 Fax:+27 12 420 5800 Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] - The software required Windows XP or better ... so I installed Linux --- This SF.Net email is sponsored by: NEC IT Guy Games. How far can you shotput a projector? How fast can you ride your desk chair down the office luge track? If you want to score the big prize, get to know the little guy. Play to win an NEC 61 plasma display: http://www.necitguy.com/?r=20 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Making animations
Hi Can a file containing multiple protein structures (e.g. NMR structures in a .pdb file) be used in animations in Jmol? From the documentation is seems I can (at least a .pdb file) but when I load a file containing multiple instances of the same protein I get a blank screen in Jmol. What must the delimiters between consecutive protein stuctures in a .pdb file be? Thanks!! -- Tjaart de Beer Bioinformatics and Computational Biology Unit Department Biochemistry FABI Square/Bioinformatics building Faculty of Natural Sciences University of Pretoria Lynwood rd Pretoria South Africa 0001 Tel:+27 12 420 5802 Cell: +27 83 504 7914 Fax:+27 12 420 5800 Email: [EMAIL PROTECTED] [EMAIL PROTECTED] [EMAIL PROTECTED] - The software required Windows XP or better ... so I installed Linux --- This SF.Net email is sponsored by Oracle Space Sweepstakes Want to be the first software developer in space? Enter now for the Oracle Space Sweepstakes! http://ads.osdn.com/?ad_id=7393alloc_id=16281op=click ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
