AutoDep 2.0 release

Dawei Lin lin at PDB.PDB.BNL.GOV
Wed Oct 22 22:50:18 EST 1997

Dear All,

The PDB is pleased to announce the release of AutoDep 2.0.  This is an improved
version of our Web-based submission procedure, with many new features and
extended validation added.

All new submissions will use AutoDep 2.0.  However, submissions already
begun with AutoDep 1 will be completed with the earlier interface.  This
will be handled automatically by the program just by continuing an AutoDep
session of a BNL-number and password initiated in AutoDep 1.  If you prefer
to try AutoDep 2.0 instead, use the "Based on a previous submission"
function to start a new session based on the uncompleted AutoDep 1
session.  After two months, all submissions will be directed to AutoDep

We wish to acknowledge the valuable contribution to this effort made by our
beta testers, our collaborators Kim Henrick at EBI, John Markley and Eldon
Ulrich at the BioMagResBank (BMRB), and the many users of AutoDep 1 who have
taken the time to send us their suggestions and bug reports.

In addition, We need to point out for those unable to access AutoDep, that
the PDB will no longer be accepting any PDB Deposition Form older than
version 3.30.  After November 1, 1997, submissions received on earlier
versions of the Deposition Form will be returned to the author, along with
the latest Deposition Form, for resubmission.  Also, those submissions
that come in the form of a PDB entry accompanied by a minimally-completed
PDB Deposition Form will be put through a syntax checking program.  If the
entry fails this check, it will be returned to the author along with
instructions needed to make it into an acceptable entry before we can
issue an ID code.

New features of AutoDep 2.0 include:

     * A Control Panel allows faster navigation.

     * Sending files is much easier through the use of a Web form with a
     file browser for selecting and uploading files to the PDB.

     * Improved helps.

     * Non-standard space groups are handled properly.

     * After the submission is complete, PDB validates the entry by running
     our internal validation programs as well as WHAT_CHECK by R.W.W. Hooft,
     G. Vriend, and C. Sander, developed in collaboration with Enrique Abola at
      PDB (  The author
     reviews these diagnostics before completing the submission.

     *Other Program Changes - Code was rewritten to:
        * fix bugs;

        * increase the number of records and fields being properly merged into
          the AutoDep form;

        * add new refinement remark templates for CNS, REFMAC;

        * automatically send data files to BMRB for processing and annotation;

        * automatically generate a more complete PDB file, including increased

        * and to make the code transportable to other sites.

If you have any questions about this new policy or on AutoDep, please
contact the PDB Help Desk at pdbhelp at or 516-344-6356 and we will be
happy to help you.

Thanks all,

 Nancy Oeder Manning                  Protein Data Bank
 Head User Support                    Brookhaven National Laboratory
 oeder at                        Biology Department, Bldg. 463
 (516) 344-5744 phone                 P.O. Box 5000
 (516) 344-5751 FAX                   Upton, NY 11973-5000   USA

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