[OpenMMS] using pdbase for loading files in MySQL

Thomas Juettemann T.Juettemann at sms.ed.ac.uk
Mon Mar 19 13:27:27 EDT 2007

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 \
    -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 \

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:


I tried "Load all entries in Manifest" but just received file not found 

Then I tried to load files in


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,

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