<br><br><div><span class="gmail_quote">On 08/10/2007, <b class="gmail_sendername">Björn Thorwirth</b> <<a href="mailto:thorwirth@fh-bingen.de">thorwirth@fh-bingen.de</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hi all!<br>Has anyone experiences with the remediated pdb archive? I've updated my<br>local mirror to it. First obvious change, is that there are now again<br>gnuZipped files. Another differece seems to be in the Manifest
<br>structure. On my pdb server pdbase dosen't find any files with the new<br>manifest. Has anyone similar experience? Or a solution?</blockquote><div><br>Hi Björn<br><br>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;
<br><br><a href="https://lists.sdsc.edu/pipermail/pdb-l/2007-September/004104.html">https://lists.sdsc.edu/pipermail/pdb-l/2007-September/004104.html</a><br><br>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 entries;
<font color="#ff0000"><br><br>1htq</font> (file too large for parsing)<font color="#ff0000"><br>2hyn</font> (file too large for parsing)<font color="#ff0000"><br>2ad1</font> (CifParseException line 444)<font color="#ff0000">
<br>2etg</font> (CifParseException line 493)<font color="#ff0000"><br>2gwh</font> (CifParseException line 630)<font color="#ff0000"><br>2i2q</font> (Data truncation: Data too long for column 'date_author_approval')
<br><br><br>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.<br><br>All the Best,<br><br>Dan.<br><br>
<br>P.S. Here is the Rsync command that we use to sync the latest remediated data;<br><br># Your config (change)<br>RSYNC= # location of local rsync<br>MIRRORDIR=.../DBd/PDB # your top level mirror directory<br><br># Remote config (don't change)
<br>SERVER=<a href="http://rsync.rcsb.org">rsync.rcsb.org</a> # remote server name (don't add '::stuff')<br>PORT=33444 # rsync port the remote server is using<br><br># Use the following to get a specific sub directory if necessary
<br># (don't forget to exclude the trailing slash!)<br>GRAB="." # Get everything<br>#GRAB=data/structures/divided/pdb # Get a sub directory<br>#GRAB=data/structures/divided/pdb/da # Get a sub directory<br><br>
$RSYNC \<br> --archive \<br> --verbose \<br> --compress \<br> --delete \
<br> --exclude=WARNING \<br> --exclude=rsync.log \<br> --exclude=<a href="http://rsyncPDB-v1.0.sh">rsyncPDB-v1.0.sh</a> \<br> --exclude=data/structures/unzipped \
<br> --port=$PORT \<br> $SERVER::ftp/$GRAB/ \<br> $MIRRORDIR/$GRAB<br><br></div><br><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Regards Björn Thorwirth<br><br><br>_______________________________________________<br>OpenMMSusers-general mailing list<br><a href="mailto:OpenMMSusers-general@bioinformatics.org">OpenMMSusers-general@bioinformatics.org</a>
<br><a href="https://bioinformatics.org/mailman/listinfo/openmmsusers-general">https://bioinformatics.org/mailman/listinfo/openmmsusers-general</a><br></blockquote></div><br><br clear="all"><br>-- <br>hello