I was at the PDB from 1974 - 1998 and closely involved with
processing entries 15 to ~9000. We also designed the "PDB
format". My replies were based on what was done for those 24
years and I cannot address what is currently being done at the PDB.
I do not know if the current PDB staff follows this bulletin
board and I can only suggest that you take this matter up
with the current PDB management, the community, and the PDB
advisory board.
Frances
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On Fri, 19 Sep 2008, Linda Brinen wrote:
I'm actually pleased to read your response and interpretation of what is
allowable and why, Frances. However, it's it pretty stark contrast to what I
was told about 18 months ago when I struggled (and eventually lost) to
preserve a numbering scheme that had a long standing historical and
literature precedence when submitting a new structure to the PDB.
This was a two-domain protein; the first domain - according to historical
numbering - had a number plus a letter code to indicate the domain; the
second domain, which started again with the number 1 - had no letter code.
We were told that that was not allowed. We wanted to preserve insertions and
deletions as well, but were also strongly discouraged, if not flat out told
we could not. While it's not usually prudent to quote offline e-mail
exchanges, I'm going to snip pertinent pieces of the discussion (I'm leaving
the original spelling errors and text bolding in place) with no indication
of the annotator who wrote these guidelines to our group. Here's part of one
of the many 'exchanges' that was had:
"I understand your point and that certain close research communities have
certain habits and traditions but the PDB serves to the whole community of
structural biology, bioinformatics, to many educators, students... In all
these cases, the simplest possible numbering of sequences, ideally numbering
identical to the numbering used by the UNP sequence database, is far the most
useful because easiest to understand. I do not say this because it is in our
manuals and help pages but because I have eight years of experience with
annotation of all kinds of structures. I would therefore very much like to
ask you to reconsider the way how you number your protein, your numbering
schema is *interpretation* more than a mere labeling schema. Needles to say,
no sequence numbering can satisfy this ambition...from my point of view,
especially the jump from 96P back to 1 will cause a lot of confusion and
misunderstanding....look at the problem from a standpoint of a general
naturalist instead of an narrow protease community"
This left us with a mandated 'start from 1 and number sequentially' format
that did exactly the opposite of what you, Frances, correctly mention as
important in any numbering scheme: preserve relationships with other
proteins. We've had to resort to providing 'translation tables' that
identify what people were expecting to see as numbers for active site
residues which now have new and non-sensical numbering. Is it the end of
the world? Of course not. But neither is it necessarily the best scientific
or logical presentation.
At the risk of inciting a rather....animated...dialogue on this topic, what
has your experience been with this kind of thing (i.e., were we just
unlucky??) and do current practices make sense and serve the community??
-Linda
Frances C. Bernstein wrote:
All entries list atoms starting at the N-terminus (or 5') so
connectivity goes in the order of the atoms in the file -
obviously with the possibility of unconnected portions
where the density is inadequate.
The entire philosphy of allowing numbering other than 1 - N
had to do with preserving relationships with other proteins.
The most common use relates to having an initial sequence 1 - N
and then a similar sequence from another species with insertions
and/or gaps. People wanted to be able to talk about the active
site (which was preserved) using the same residue numbers.
Negative numbers came up with additions at the N-terminus.
Offhand, I don't recall why descending numbers were used but
I believe that there is at least one such entry.
Frances
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On Fri, 19 Sep 2008, Ian Tickle wrote:
But what connectivity would be implied by descending numbers: the order
in the file or the order of the numbering? I assume the former,
otherwise what would be the point of having descending numbering? And I
wonder how many programs would baulk at it (or even at ascending
negative numbers?).
-- Ian
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On
Behalf Of Frances C. Bernstein
Sent: 19 September 2008 16:44
To: Todd Geders
Cc: [email protected]
Subject: Re: [ccp4bb] Non-sequential residue numbering?
As long as each residue within a chain has a unique identifier
(residue number plus insertion code), there is no restriction
on numbering. The numbers can be in ascending or descending
order, non-sequential, and even negative.
Frances
=====================================================
**** Bernstein + Sons
* * Information Systems Consultants
**** 5 Brewster Lane, Bellport, NY 11713-2803
* * ***
**** * Frances C. Bernstein
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On Fri, 19 Sep 2008, Todd Geders wrote:
Hello all,
I have a structure from a non-natural fusion of the truncated
C-terminus
of
one protein with the truncated N-terminus of another. For the
deposition, we
want to keep the numbering as found in the separate proteins. It
looks
something like this:
1 12
| |
....HWVCKDIALLMCFFLEEMSEEP....
| |
754 763
At no point is there an overlap in numbering (i.e. the N-terminal
residue
number is higher than the C-terminal residue number).
Is this numbering scheme supported by the PDB standard? Thus far,
all
of the
software seems to handle it (refmac, Coot, PyMOL, pdb_extract, PDB
precheck &
validation, etc).
Can anyone see a reason to not deposit with this non-sequential
residue
numbering?
~Todd
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