> Hi, > > I have been using Jmol very succesfully to allow the display of > structures stored in .pdf format on an internal company webpage. I > would now like to extend this site to include structures that are > available as .cif.
To the best of my knowledge, Jmol will read all .cif files, including .mmcif files published by the PDB (be advised that some of the the .mmcif files published by the PDB have errors and are not the same as the corresponding .pdb file) However, the Jmol CifReader does not support all CIF features, and it is possible that you have a conforming .cif file that Jmol is not reading correctly. > Although I could convert them to .pdb before I add > them to the site I would prefer to load the .cif directly. Unfortunately > using the same scripts to load a .cif fails with no obvious errors on > either the server or client although if one has a Jmol console open one > gets the following output: > > Jmol executing script ... > File Error:Could not read file:java.util.NoSuchElementException > ScriptException:Could not read file:java.util.NoSuchElementException > Script line:load small_molecule/mymol/mymol.cif > ScriptException:Could not read file:java.util.NoSuchElementException > Script line:load small_molecule/mymol/mymol.cif > Jmol script completed > > I'm unfortunately not able to share this .cif, which was generated in > ShelX, with you, Well, what in the world do you expect *me* to do? ;-) I suggest that you create another file that is not so valuable using the same tools and see if it fails. One that you can send to me. The smallest file that reproduces the problem would be best. OR change all the atom types and send it to me. I am not a chemist and could not figure it out anyway ;-) OR send me a contract and a non-disclosure agreement so that you can have some legal protection before I look at your special file. > but the structure does load into Jmol once converted to > .pdb and is readable by both Mercury and DS Viewer so it appears not to > be corrupt. The problem sounds analagous to that described by Todd > Beverly at the end of last year except that I'm using jmolScript(load > small_molecule/mymol/mymol.cif) rather than using jmolAppletInline. I believe that Todd Beverly's problems were resolved. > Any suggestions on resolving the problem would be appreciated. The ball is in your court. You need to reproduce the problem with a small file that you can send to me. Miguel ------------------------------------------------------- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
