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You can use PDBML right now if you wish, but first you need to be sure
the software you want to use is ready for it.
On the question of extending the PDB format -- of course you can, but
again, you need to have software to process it with your favorite
extensions.
That is why the PDB format is alive and well -- a lot of software
can process it and produce it. In addition, the PDB format, the
mmCIF format, and PDBML have all changed and most likely will
continue to change, hopefully in a well-coordinated manner.
To move solidly to a new format smoothly you need:
1. Fairly broad community agreement on what that format is; and
2. Software developers ready, willing and able to create the software
you need to use that new format.
It takes a lot of collegial discussion and a major investment of
resources to do this, but it can be done. There does not yet
seem to be broad agreement on what format that should be, and
it is hard to find funding and willing developers to make the
transition. Maybe we need to talk some more about what formats
have better or worse in what ways to achieve the consensus needed
to do what may need to be done.
-- H. J. Bernstein
At 8:20 PM +0200 5/18/06, Flip Hoedemaeker wrote:
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<flame> Shouldnt we adopt XML as a new standard to replace both PDB and
mmCIF, to have finally a flexible but universal format? </flame>
Flip (Pinin' for the Fjords)
...
On Thursday 18 May 2006 10:31 am, [EMAIL PROTECTED] wrote:
A question for the group: is there any push to get TLS parameters
incorporated into the standard PDB data format?
The PDB format is dead, it's passed on! This format is no more!
It has ceased to be! It's expired and gone to meet its maker!
If you hadn't wired it into the code of many programs it would be
pushing up the daisies!
No, really. Extensions to the PDB format itself are highly unlikely. It
exists as a legacy intermediate to the underlying archival mmCIF-derived
database info. The TLS parameters are correctly described there, and are
correctly translated into PDB format (yes, in a REMARK record) on demand.
--
=====================================================
Herbert J. Bernstein, Professor of Computer Science
Dowling College, Kramer Science Center, KSC 121
Idle Hour Blvd, Oakdale, NY, 11769
Office: +1-631-244-3035
Lab (KSC 020): +1-631-244-3451
[EMAIL PROTECTED]
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