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

Thomas Juettemann T.Juettemann at sms.ed.ac.uk
Wed Mar 21 07:20:39 EDT 2007


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
>> >>
>> >
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>>
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>
>
> -- 
> hello
>


----- End message from dan.bolser at gmail.com -----





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