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Clemens Vonrhein wrote:
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On Thu, May 18, 2006 at 10:58:52AM -0700, Ethan Merritt 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.
Formats exists to make a specific task easy and understandable. To me
there is a distinction between a working format and a storage/archival
format - since archival of data (consisting of coordinates as well as
a lot of meta-information) is a very different task from working with
X, Y, Z, OCC, B (and a few other things).
I don't think the 'one size fits all' approach works well in this
case: PDB might be bad for archival but it is easy as a working
format, whereas mmCIF is probably great for databases (I'm no expert
there) but I find it difficult to use as a working format.
Cheers
Clemens
Amen!
I've seen only one CIF come through my lab in the last few years
(without trying to avoid them) and that was when a colleague asked me to
convert it to PDB format. I know how much work has gone into the mmCIF
format and I see the value of having a full description of the
experiment and its context, but for daily use the PDB format is still
very much alive.
Bart
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