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{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Cannot parse pdb file. ","articleBody":"Hi, \r\n\r\nit seems that I cannot parse any pdb file using PDBFileReader. \r\nThis simple code fails for me (2src_off.pdb is official 2src PDB file from RCSB):\r\n\r\n```java\r\n    PDBFileReader pdbReader = new PDBFileReader();\r\n    //pdbReader.getFileParsingParameters().setCreateAtomCharges(false);\r\n    String path = \"~/pranklib/2src_off.pdb\";\r\n    Structure structure = null;\r\n    try {\r\n      structure = pdbReader.getStructure(path);\r\n      System.out.println(structure);\r\n    } catch (IOException e) {\r\n      e.printStackTrace();\r\n    } \r\n```\r\n\r\n\r\nwith error:\r\n\r\n```\r\n20:22:57 [main] ERROR org.biojava.nbio.structure.io.mmcif.SimpleMMcifParser - This does not look like a valid mmCIF file! The first line should start with 'data_', but is: 'null'\r\nException in thread \"main\" java.lang.NullPointerException\r\n        at org.biojava.nbio.structure.io.ChargeAdder.addCharges(ChargeAdder.java:55)\r\n        at org.biojava.nbio.structure.io.PDBFileParser.addCharges(PDBFileParser.java:2772)\r\n        at org.biojava.nbio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2760)\r\n        at org.biojava.nbio.structure.io.PDBFileParser.parsePDBFile(PDBFileParser.java:2622)\r\n        at org.biojava.nbio.structure.io.PDBFileReader.getStructure(PDBFileReader.java:307)\r\n        at org.biojava.nbio.structure.io.LocalPDBDirectory.getStructure(LocalPDBDirectory.java:337)\r\n        at org.biojava.nbio.structure.io.LocalPDBDirectory.getStructure(LocalPDBDirectory.java:321)\r\n        at hello.HelloWorld.main(HelloWorld.java:22)\r\n```\r\n\r\nWeird thing is that it didn't fail before. How is that possible? Also we do I get so many ERROR from MMcifParser when I am parsing PDB and not mmCIF?\r\n\r\nThanks in advance for any help.\r\n\r\nLukas","author":{"url":"https://github.com/jendelel","@type":"Person","name":"jendelel"},"datePublished":"2017-08-30T18:25:42.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":23},"url":"https://github.com/702/biojava/issues/702"}