Thanks, Andrew, that history helps. And I must say, the hybrid-36 scheme
really is very clever. You would probably like the base-90 scheme I cooked
up for the JVXL surface file format.
Unlike Peter, I have no problem with custom specifications, as long as they
are clear, unambiguous, and published. Something like this should not have
to be "discovered" 100,000 lines into a file. It would have been immensely
helpful if there had been a required REMARK record to the effect that atom
numbers/residue numbers were in some specific format. Far too often someone
comes up with a solution to their problem for their program and implements
it without ever considering how it might impact other programs. As it is,
Jmol, for instance, with some tweaks, can now read a file with both the
hybrid-36 and Schroedinger's HEX solution (upon the next release), but it
involves additional checking just to be able to be on the look-out for this
issue, and that potentially slows down all PDB file reading by Jmol (or any
other program).
Bob
On Sun, Jan 20, 2013 at 8:14 PM, Andrew Dalke <da...@dalkescientific.com>wrote:
> On Jan 20, 2013, at 1:08 PM, Andrew Dalke wrote:
> > For kicks, I pulled up my copy of the PDB format from 1974. It says that
> > the PDB file has: COMPND, AUTHOR, CRYST1, DECODE, REMARK
>
> Err, that was supposed to be deleted. I found that I didn't have a complete
> spec, dug through the old PDB newsletters, looked for old printouts in my
> files, couldn't find it, got distracted, and managed to forget to delete
> these two lines.
>
> So I don't know if the 1970s spec says that those files were supposed to
> be in every PDB file, but I'm pretty certain that they were in every file
> that they distributed.
>
> Andrew
> da...@dalkescientific.com
>
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Chemistry Department
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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