A few months ago, I had a similar experience as Linda Brinen that the
PDB is not very accommodating towards depositors wishes to put it
mildly. I have the impression that after many Journals are not only
requiring a PDB code as proof that the coordinates are deposited but
also mandate proof that the coordinates have been released for public
access, the PDB has become significantly less willing to listen to
depositors.
My question: do more people have similar experiences, or are Lindas and
mine isolated cases? From the reaction by Jasimine Young I get the
impression that not all annotators apply the same rules. If cases like
this happen more often we could ask the pdb clarify the rules and
especially clarify how cases are handled when the annotator and
depositor have different opinions.
Best regards,
Herman
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of
Frances C. Bernstein
Sent: Friday, September 19, 2008 8:34 PM
To: [log in to unmask]
Subject: Re: [ccp4bb] Non-sequential residue numbering?
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
>> =====================================================
>> **** Bernstein + Sons
>> * * Information Systems Consultants
>> **** 5 Brewster Lane, Bellport, NY 11713-2803
>> * * ***
>> **** * Frances C. Bernstein
>> * *** [log in to unmask]
>> *** *
>> * *** 1-631-286-1339 FAX: 1-631-286-1999
>> =====================================================
>>
>> 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: [log in to unmask]
>>>> [mailto:[log in to unmask]]
>>> On
>>>> Behalf Of Frances C. Bernstein
>>>> Sent: 19 September 2008 16:44
>>>> To: Todd Geders
>>>> Cc: [log in to unmask]
>>>> 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
>>>> * *** [log in to unmask]
>>>> *** *
>>>> * *** 1-631-286-1339 FAX: 1-631-286-1999
>>>> =====================================================
>>>>
>>>> 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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>
>
> --
> Linda S. Brinen
> Adjunct Assistant Professor
> Dept of Cellular & Molecular Pharmacology and The Sandler Center for
> Basic Research in Parasitic Diseases
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