Bugs item #988592, was opened at 2004-07-10 11:58 Message generated for change (Comment added) made by nobody You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=988592&group_id=23629
Category: Applet Group: None Status: Open Resolution: None Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: cif issues Initial Comment: There is one more important CIF format that Jmol needs to be able to read. This comes from the Inorganic Crystal Structure Database, http://www.fiz-informationsdienste.de/en/DB/icsd/ For an example, see http://www.stolaf.edu/people/hansonr/jmol/cif/viewdir.ht m and select "ic1166.cif" To download the file, check for it at http://www.stolaf.edu/people/hansonr/jmol/cif Basically, this is a slight variant of the Cambridge Crystal Structure Database. Mostly the format of the atom information is different. I note that in this file there can be atoms designated with no coordinates! So we have here: Re1 Re3+ 4 e 0.0736(1) -.00119(7) 0.07901(8) 0. 1. Re2 Re3+ 4 e 0.4356(1) 0.06192(7) 0.45604(8) 0. 1. Cs1 Cs1+ 4 e 0.3809(2) 0.3961(2) 0.3240(2) 0. 1. Cs2 Cs1+ 4 e 0.1175(2) -.3131(1) -.0456(1) 0. 1. Cl1 Cl1- 4 e 0.2775(7) -.0799(4) 0.0192(5) 0. 1. Cl2 Cl1- 4 e -.0577(8) 0.0757(5) 0.2110(5) 0. 1. Cl3 Cl1- 4 e -.2203(7) 0.0564(4) 0.5429(5) 0. 1. Cl4 Cl1- 4 e 0.3159(7) -.0246(4) 0.3056(5) 0. 1. Cl5 Cl1- 4 e 0.4982(7) 0.2012(4) 0.5660(5) 0. 1. Cl6 Cl1- 4 e 0.1978(7) 0.1484(4) 0.0706(5) 0. 1. Cl7 Cl1- 4 e 0.0166(7) -.1522(4) 0.1619(5) 0. 1. Cl8 Cl1- 4 e 0.5887(7) 0.1235(5) 0.3295(5) 0. 1. O1 O2- 4 e 0.272(4) 0.194(2) 0.338(3) 9.6 1. H1 H1+ 4 e 0. 2. Note the H1 H1+ line has no coordinate. A single space is being used, not just generic white space, to separate fields. The error given is: Java(TM) Plug-in: Version 1.4.0_01 Using JRE version 1.4.0_01 Java HotSpot(TM) Client VM User home directory = C:\Documents and Settings\hansonr Proxy Configuration: Browser Proxy Configuration FileManager.openFile(icsd_1166.cif) SmarterModelAdapter:The model resolver thinks:Cif java.lang.NullPointerException at org.jmol.adapter.smarter.ModelReader.parseFloat (ModelReader.java:45) at org.jmol.adapter.smarter.CifReader.processAtomSiteLoopB lock(CifReader.java:288) at org.jmol.adapter.smarter.CifReader.processLoopBlock (CifReader.java:144) at org.jmol.adapter.smarter.CifReader.readModel (CifReader.java:65) at org.jmol.adapter.smarter.ModelResolver.resolveModel (ModelResolver.java:57) at org.jmol.adapter.smarter.SmarterModelAdapter.openBuffe redReader(SmarterModelAdapter.java:55) at org.openscience.jmol.viewer.managers.FileManager$FileO penThread.openReader(FileManager.java:409) at org.openscience.jmol.viewer.managers.FileManager$FileO penThread.openInputStream(FileManager.java:402) at org.openscience.jmol.viewer.managers.FileManager$FileO penThread.run(FileManager.java:379) at org.openscience.jmol.viewer.managers.FileManager.openF ile(FileManager.java:100) at org.openscience.jmol.viewer.JmolViewer.openFile (JmolViewer.java:897) at org.openscience.jmol.viewer.script.Eval.load (Eval.java:1566) at org.openscience.jmol.viewer.script.Eval.instructionDispatc hLoop(Eval.java:337) at org.openscience.jmol.viewer.script.Eval.run (Eval.java:281) at java.lang.Thread.run(Unknown Source) error opening file:/D:/js/struc/data/csd/icsd_1166.cif java.lang.NullPointerException openFile(icsd_1166.cif) 210 ms InterruptedException! But there are more problems. The following block seems to be causing great difficulty: loop_ _atom_site_aniso_label _atom_site_aniso_type_symbol _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 Re1 Re3+ 0.0046(1) 0.00294(4) 0.00353(6) -.0008(1) 0.0005(1) -.0002(1) Re2 Re3+ 0.0049(1) 0.00264(4) 0.00456(6) 0.0005(1) 0.0019(1) 0.0005(1) Cs1 Cs1+ 0.0097(2) 0.00993(14) 0.0068(1) 0.0024(3) 0.0049(3) 0.0037(2) Cs2 Cs1+ 0.0082(2) 0.00459(9) 0.0080(1) 0.0015(3) 0.0001(3) -.0029(2) Cl1 Cl1- 0.0059(8) 0.0050(4) 0.0068(5) 0.0028(9) 0.001 (1) -.0014(7) Cl2 Cl1- 0.0104(9) 0.0054(4) 0.0049(5) 0.0007(11) 0.004 (1) -.0019(7) Cl3 Cl1- 0.0062(7) 0.0041(3) 0.0074(5) 0.0015(9) 0.004 (1) -.0006(7) Cl4 Cl1- 0.0088(8) 0.0050(4) 0.0047(4) -.0021(10) -.001 (1) 0.0011(6) Cl5 Cl1- 0.0083(8) 0.0033(3) 0.0070(5) 0.0007(9) 0.000 (1) -.0004(7) Cl6 Cl1- 0.0075(8) 0.0035(3) 0.0062(5) -.0038(9) 0.000 (1) -.0002(7) Cl7 Cl1- 0.0101(9) 0.0033(3) 0.0052(5) -.0028(9) 0.000 (1) 0.0020(6) Cl8 Cl1- 0.0100(9) 0.0053(4) 0.0056(5) -.0039(10) 0.005 (1) 0.0029(7) and charges on the type symbol is causing the atom symbol to be misinterpreted. see http://www.stolaf.edu/people/hansonr/jmol/cif/ic1166b.ci f for what this should (probably) look like. (It's not a great data set.) similarly: http://www.stolaf.edu/people/hansonr/jmol/cif/ic30516.ci f and http://www.stolaf.edu/people/hansonr/jmol/cif/ic30516b. cif Bob Hanson ---------------------------------------------------------------------- Comment By: Nobody/Anonymous (nobody) Date: 2004-07-11 10:00 Message: Logged In: NO This is an invalid CIF. CIFs have two data structures, loops and items. In a loop like this all rows must have the same number of (whitespace-separated) fields. Note that the number of fields in each row and their semantics is given by the list of names in the loop whose length must equal each row. For more information on CIF syntax, from which no deviations are allowed, see http://www.iucr.org PeterMR NB I doubt that the ICSD is emitting invalid CIFs on a systematic basis. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379133&aid=988592&group_id=23629 ------------------------------------------------------- This SF.Net email sponsored by Black Hat Briefings & Training. Attend Black Hat Briefings & Training, Las Vegas July 24-29 - digital self defense, top technical experts, no vendor pitches, unmatched networking opportunities. Visit www.blackhat.com _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
