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

[Thomas Juettemann]

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?

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?

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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