[OpenMMS] using pdbase for loading files in MySQL

[Henning Stehr]

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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