Hi Dan, yes, I recreated the DB, same error. Changing the datatype from float to real solved the problem. Changed colums: occupancy_esd density_matthews density_meas aniso_b_0_0 b_iso_max ls_percent_reflns_r_free ls_r_factor_obs ls_wr_factor_r_free occupancy_max solvent_model_param_bsol pdbx_ls_sigma_I pdbx_overall_ESU_R luzzati_coordinate_error_obs dev_ideal_target weight percent_reflns_r_free R_factor_obs_no_cutoff b_iso_wilson_estimate observed_criterion_F_max pdbx_Rsym_value percent_possible_obs Often I also changed groups, eg: colum mentioned above: ls_r_factor_obs Changed colums: ls_r_factor_all REAL, ls_r_factor_obs REAL, ls_r_factor_r_free REAL, ls_r_factor_r_free_error REAL, ls_r_factor_r_free_error_detai TEXT, ls_r_factor_r_work REAL, ls_r_fsqd_factor_obs REAL, ls_r_i_factor_obs REAL, If anyone is interested in the changed CreateMmsMySQL.sql, please contact me. Comments, especially about dependencies are very welcome! ;) Thomas ----- Message from dan.bolser at gmail.com --------- Date: Tue, 20 Mar 2007 22:14:30 +0100 From: Dan Bolser <dan.bolser at gmail.com> Reply-To: Dan Bolser <dan.bolser at gmail.com> Subject: Re: pdb-l: [OpenMMS] using pdbase for loading files in MySQL To: Thomas Juettemann <t.juettemann at sms.ed.ac.uk> > 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 > ----- End message from dan.bolser at gmail.com -----