[OpenMMS] setting up mmCIF database using OpenMMS

Dan Bolser dan.bolser at gmail.com
Thu Sep 18 06:20:20 EDT 2008

Sorry, I have forgotten the implementation details here.

I have CCed this to my college Henning, who might be more helpful...


2008/9/18 Thomas Juettemann <t.juettemann at sms.ed.ac.uk>:
> Hi WK Yeo,
> I am cc'ing Dan, he might be more helpful, I have not worked with
> mmCIF for a while. I attached my correction script. I remember that I
> had also trouble with the Java classpath, if Dan can't recall I am
> looking into it again!
> Cheers,
> Thomas
> On Tue, Sep 16, 2008 at 10:54, Wee Kiang Yeo <weekiang at gmail.com> wrote:
>> Hi, Thomas,
>> I am at the initial stages of learning how to load PDB structural data
>> into mySQL databases. I just read your write-up on setting up mmCIF
>> database using OpenMMS.
>> http://www.bioinformatics.org/pipermail/openmmsusers-general/2007-March/000006.html
>> 1) The documentation says that /run/unix/pdbase is a shell script
>> which invokes PDBase.java. However, since I am not familiar with Java,
>> I did not understand how you managed to start the shell script or
>> PDBase.java.
>> 2) Also, I would appreciate it if you can inform me regarding when I
>> should input those parameters after the java command? I am also quite
>> clueless about how to link to the package org.rcsb.openmms.apps.rdb
>> 3) When I typed ./pdbase, I received the following Java exceptions:
>> Exception in thread "main" java.lang.NoClassDefFoundError:
>> org/rcsb/openmms/apps/rdb/PDBase
>> Caused by: java.lang.ClassNotFoundException: org.rcsb.openmms.apps.rdb.PDBase
>> 4) I would love to have a copy of the perl script which you've
>> mentioned in the posting.
>> Thank you very much for your help.
>> Regards,
>> WK Yeo


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