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[Jmol-developers] [ jmol-Bugs-2802210 ] CIF read error?
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From: SourceForge.net <no...@so...> - 2009-06-10 18:59:17
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Bugs item #2802210, was opened at 2009-06-06 10:46 Message generated for change (Comment added) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2802210&group_id=23629 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: File Input/Output Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Simon Westrip (publcif) Assigned to: Miguel (migueljmol) Summary: CIF read error? Initial Comment: I am experiencing CIF read errors, possibly related to an earlier bug "cif read error - ID: 1877855" if I download a CIF from the IUCr's website, then upload to a Jmol tool (e.g. the IUCr's jmol toolkit), I get the 'unrecognzed fie format' message. This only occurs on LINUX and MAC (windows is OK -for a change!) However, if I remove the comment section from the start of the CIF (or just add a 'dummy' data block before the comment section), Jmol has no problems recognizing it. There's nothing obvious in the 'offending' comment section (to me anyway). A further curiosity is that when I test the same CIFs using my 'localhost' server, everything is OK. I've been using Jmol 11.6.x - I havnt tested the development versions yet. You should be able to see this behaviour if you look at http://www.publcryst.co.uk/demos/jmol/sup_bug.php?issue=06&cifid=br2107 (using Firefox on Linux or Mac - even if model loads first time, it probably wont if you reload) I'm not sure if this is a Jmol bug or a peculiarity of how the browser caches the CIF, or ...? (NB Opera on linux is OK) Anyway, I think its probably worth reporting just in case anyone else experiences problems with these CIFs ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2009-06-10 18:59 Message: Thanks for this. Cheers Simon ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-06-10 18:12 Message: one additional comment -- you will want to load those files using the load filename.cif {nnn mmm 0} option because of the way the bonds and atom positions are in the file. ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-06-10 18:11 Message: this is corrected in Jmol 11.7.42 and Jmol 11.6.25 See files at http://chemapps.stolaf.edu/jmol/docs/examples-11 ---------------------------------------------------------------------- Comment By: Simon Westrip (publcif) Date: 2009-06-09 08:36 Message: Sample CIF from IUCr website is attached Cheers Simon ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2009-06-09 04:42 Message: please send an example file that causes the problem. I suspect it is because the header is more than 16 lines, and Jmol can't resolve it properly. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=2802210&group_id=23629 |