Bugs item #988592, was opened at 2004-07-10 11:58 Message generated for change (Tracker Item Submitted) made by Item Submitter 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 ---------------------------------------------------------------------- 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
