[OpenMMS] remediated PDB-Archive

Dan Bolser dan.bolser at gmail.com
Tue Oct 9 06:28:06 EDT 2007

On 08/10/2007, Björn Thorwirth <thorwirth at fh-bingen.de> wrote:
> Hi all!
> Has anyone experiences with the remediated pdb archive? I've updated my
> local mirror to it. First obvious change, is that there are now again
> gnuZipped files. Another differece seems to be in the Manifest
> structure. On my pdb server pdbase dosen't find any files with the new
> manifest. Has anyone similar experience? Or a solution?

Hi Björn

Other than the .Z -> .gz difference we have not had any difficulty migrating
to the remediated files. However, I did read about a problem that sounds
related to the manifest files to do with listing all files;


This could be a problem if you create an FTP manifest from a direct FTP
connection (using some FTP clients). Locally we use Rsync, and I believe we
create our own manifest that specifically excludes the following PDB

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')

Sorry I can't send more details. Can you try generating your own manifest
file directly from the PDB files that you downloaded, let us know if it
fixes the problem.

All the Best,


P.S. Here is the Rsync command that we use to sync the latest remediated

# Your config (change)
RSYNC= # location of local rsync
MIRRORDIR=.../DBd/PDB # your top level mirror directory

# Remote config (don't change)
SERVER=rsync.rcsb.org # remote server name (don't add '::stuff')
PORT=33444 # rsync port the remote server is using

# Use the following to get a specific sub directory if necessary
# (don't forget to exclude the trailing slash!)
GRAB="." # Get everything
#GRAB=data/structures/divided/pdb # Get a sub directory
#GRAB=data/structures/divided/pdb/da # Get a sub directory

$RSYNC                                          \
    --archive                                   \
    --verbose                                   \
    --compress                                  \
    --delete                                    \
    --exclude=WARNING                           \
    --exclude=rsync.log                         \
    --exclude=rsyncPDB-v1.0.sh                  \
    --exclude=data/structures/unzipped          \
    --port=$PORT                                \
    $SERVER::ftp/$GRAB/                         \

Regards Björn Thorwirth
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