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[Savannah-register-public] [task #14528] Submission of relax

From: Edward d'Auvergne
Subject: [Savannah-register-public] [task #14528] Submission of relax
Date: Tue, 17 Jul 2018 03:52:49 -0400 (EDT)
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:52.0) Gecko/20100101 Firefox/52.0

Follow-up Comment #34, task #14528 (project administration):

Sorry for the delay, I have just returned from holidays.

> These are text files (as well as AUTHORS), they should include the notices.
README is only a fallback for binary files.

The PDB text file format is very rigid, it is a strict fixed-columnar
formatted text file
For example this structure distributed with relax:

- 1OSA Protein Data Bank entry <>.
- 1OSA PDB file <>.

The original copyright holders prior to the content being made public domain
could theoretically be added to the PDB REMARK sections.  However the REMARK
section numbering and format can be important - although they can be in free
form, in many cases intricate, automated, software-specific formatting is used
that simple hand edits could easily break.  Also, as discussed previously
<>, we absolutely cannot
identify the original copyright holder.  This task is impossible with the
design of the public domain Protein Data Bank, as neither the PDB nor the
original scientific publication identify the original copyright holder.  This
can sometimes be in the AUTHOR record, but again this could simply be the name
of the supervisor, the lead scientist (as in the 1OSA example), or all the
authors rather than the original copyright holder.  In the almost 50 year
history of the PDB, recording the true original copyright holder(s) has not be
considered important, as that person(s) has waived their copyrights.  In
science, it is all the authors of the original paper that matter - and all
those authors are credited in the PDB database files in the JRNL AUTH record.

In the case of our software relax, most PDB files are used in the test suite
fall into two categories:

1) Those that are deliberately unmodified from the originals found in the
Protein Data Bank database <>.  This is so that we
can forever test that we can correctly read the format.  Being able to read
modified PDB files does not guarantee that we can correctly read the

2) Those PDB files that are generated either by relax or by other software. 
Again we need to test that the unmodified original can be read correctly.  For
a few tests, we read the PDB file generated by relax into internal data
structures, output a new PDB file, and check that the diff is zero.

We believe that having public domain statements (not identifying the
pre-copyright-waiver owners), as well as copyright notices, in an accompanying
README file is the correct way to handle PDB text files:

- test_suite/shared_data/structures/README

> WRT the GFDL, I'm not sure. Perhaps you'll have to speak to

I will try corresponding with RMS and the FSF licensing department.


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