pdb-l: [OpenMMS] using pdbase for loading files in MySQL

Dan Bolser dan.bolser at gmail.com
Tue Mar 20 17:14:30 EDT 2007


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
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >> OpenMMSusers-general at bioinformatics.org
> >> https://bioinformatics.org/mailman/listinfo/openmmsusers-general
> >>
> >
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