On 20/03/07, Thomas Juettemann <t.juettemann at sms.ed.ac.uk> wrote: > Henning, > > many thanks! > > The unzipped files worked, but caused another error: > > ********** LOAD ENTRY FAILED ********** > SQL Exception in DBLoader.loadEntries() > while loading Entry PDB_ID=5RSA > Exception Description: java.sql.BatchUpdateException: Data > truncation: Out of range value adjusted for column 'occupancy_esd' at row 1 > SQL Message: Data truncation: Out of range value adjusted for > column 'occupancy_esd' at row 1 SQL State: 01004 SQL ErrorCode: 0 > Stack Trace > java.sql.BatchUpdateException: Data truncation: Out of range value > adjusted for column 'occupancy_esd' at row 1 > at > com.mysql.jdbc.PreparedStatement.executeBatchSerially(PreparedStatement.java:1213) > at > com.mysql.jdbc.PreparedStatement.executeBatch(PreparedStatement.java:912) > at > org.rcsb.openmms.dbinsert.InsertEntry.insert_ATOM_SITE(InsertEntry.java:2821) > at > org.rcsb.openmms.dbinsert.InsertEntry.insertEntryData(InsertEntry.java:766) > at > org.rcsb.openmms.apps.rdb.InsertEntryFinal.buildAndInsertEntry(InsertEntryFinal.java:156) > at > org.rcsb.openmms.apps.rdb.DBLoader.insertSingleEntry(DBLoader.java:462) > at > org.rcsb.openmms.apps.rdb.DBLoader.processSingleEntry(DBLoader.java:391) > at > org.rcsb.openmms.apps.rdb.DBLoader.loadSingleEntry(DBLoader.java:265) > at > org.rcsb.openmms.apps.rdb.DBLoader.loadEntries(DBLoader.java:249) > at > org.rcsb.openmms.apps.rdb.PanelSet$4.construct(PanelSet.java:617) > at > org.rcsb.openmms.apps.rdb.SwingWorker$2.run(SwingWorker.java:111) > at java.lang.Thread.run(Unknown Source) > > ********** end of exception report ********** > > I used 1FNT and 5RSA as example, both triggered the same error. > Is there a change in the scheme / mmCIF format? Did you try dropping and recreating the database since getting the loader to behave? There is a chance that the previous failures left some junk in the tables. > > I would also be interested in peoples' opinion about the mmCIF format. I > got the feeling that the mmCIF format was suggested/introduced a while > ago and still hasn't made the breakthrough, or? Will it prevail or is > XML here the future as well? You need to check the archive of the PDB-l mailing list. If you don't find what you need try searching with Google or email pdb-l. Dan. > > Thanks for all your help! > > Thomas > > > Henning Stehr wrote: > > Hi Thomas, > > > > The problem is that the files are compressed. You can download the > > files from the ftp site and uncompress them locally. Then set the data > > dir to file:///localdir/. This should work. If you are loading the > > whole pdb it is wise to exclude the following entries: > > > > * 1htq (file too large for parsing) > > * 2hyn (file too large for parsing) > > * 2ad1 (CifParseException line 444) > > * 2etg (CifParseException line 493) > > * 2gwh (CifParseException line 630) > > * 2i2q (Data truncation: Data too long for column 'date_author_approval') > > > > And probably give java a bit more memory if possible. I also modified > > PDBase to run in batch mode (without the gui). I might post about this > > later. Contact me if you are interested. > > > > Henning > > > > On 3/19/07, Thomas Juettemann <T.Juettemann at sms.ed.ac.uk> wrote: > >> Dear all, > >> > >> I am newbie using mmCIF files, apologies for the low level questions. > >> I am also very happy if you can point me to a tutorial or example page! ;) > >> > >> The db scheme was created correctly using CreateMmsMySQL.sql and InitMMs.sql > >> > >> I managed to start pdbase: > >> java \ > >> -classpath > >> .:/usr/java/jre1.5.0_07/lib/ext/biojava-1.4.jar:/home/tj/OpenMMS-1.5.1_Std/openmms/classes/OpenMMS.jar:/usr/java/mysql-connector-java-5.0.5/mysql-connector-java-5.0.5-bin.jar > >> \ > >> -Xmx1500M \ > >> org.rcsb.openmms.apps.rdb.PDBase \ > >> LenientParse \ > >> data=ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all \ > >> manifest=ftp://ftp.rcsb.org/pub/pdb/ls-lR \ > >> log=PDBASE.LOG \ > >> debug=5 > >> > >> The connection to my local database was fine > >> > >> First a got a connection timeout which probably comes from the wrong > >> data and manifest link. I corrected this to: > >> > >> data=ftp://ftp.rcsb.org/pub/pdb/data/structures/all/mmCIF > >> manifest=ftp://ftp.rcsb.org/pub/pdb/data/structures/ls-lR > >> > >> I tried "Load all entries in Manifest" but just received file not found > >> errors. > >> > >> Then I tried to load files in > >> > >> /home/tj/OpenMMS-1.5.1_Std/openmms/data/lists/StructureIDs.list > >> > >> I used names like: 1fnt and 1fnt.cif.Z > >> > >> but same error. > >> > >> Same with putting names manually "Load this list of entries" > >> > >> Can anyone point me to my error? > >> > >> Thanks a lot, > >> Thomas > >> > >> > >> > >> > >> > >> _______________________________________________ > >> OpenMMSusers-general mailing list > >> OpenMMSusers-general at bioinformatics.org > >> https://bioinformatics.org/mailman/listinfo/openmmsusers-general > >> > > > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > > https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . > > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . > -- hello