[OpenMMS] setting up mmCIF database using OpenMMS

[Thomas Juettemann]

Dear all,

a quick sum up of my experiences reading files into a MySQL database 
using OpenMMS (pdbase).


The standard parameters when initializing pdbase are:

java \
  -classpath 
.:./classes:./mysql-connector-java-5.0.4/mysql-connector-java-5.0.4-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 dir data=ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/all 
does not exist anymore. In out days the files just exist zipped in 
subdirectories (divided). The files have to be downloaded and unzipped 
fist. An easy way downloading bigger amounts of data is using this script:

ftp://ftp.rcsb.org/pub/pdb/software/getPdbStructures.pl
then:
gunzip -r ~/pdb0702091045/pdb/

A modified version of starting pdbase:
java \
-classpath 
.:/home/s0571283/OpenMMS-1.5.1_Std/openmms/classes/OpenMMS.jar:/home/s0571283/mysql-connector-java-5.0.5/mysql-connector-java-5.0.5-bin.jar

   -Xmx1500M \
   org.rcsb.openmms.apps.rdb.PDBase \
   LenientParse \
   data=file:///home/s0571283/positiveSet/MMS/pdb0702211233/mmCIF \
   manifest=file:///home/s0571283/ls-lR \
   log=PDBASE.LOG \
   debug=5

Next step is setting up the database.

mysqladmin create openmms

The file

./src/mms/deriv/sql/CreateMmsMySQL.sql

contains many FLOAT where REAL is needed. A simple

%s/FLOAT/REAL/


in vi solved this. After populating the database the indices should be 
recreated.

mysql openmms < ./src/mms/deriv/sql/CreateMmsMySQL.sql
mysql openmms < ./src/mms/deriv/sql/InitMms.sql

The files

./src/mms/deriv/sql/DropIndicesMySQL.sql
./src/mms/deriv/sql/CreateIndicesMySQL.sql

are not consistent with the db schema. I wrote a perl script that 
downloads the newest version of CreateMmsMySQL.sql and InitMms.sql, 
replaces all FLOAT with real and creates CreateIndices.sql and 
DropIndicesMySQL.sql. Contact me if you are interested.

mysql openmms < ./src/mms/deriv/sql/DropIndicesMySQL.sql
mysql openmms < ./src/mms/deriv/sql/CreateIndices.sql


Cheers,
Thomas