I like to think structural biologists are more than just another user 
group, they FEED the PDB!
Their needs should first and foremost be taken care off, I would think.....

Also, it would indeed be a great loss if legacy programs can not be used 
anymore.

- Jeroen -

Clemens Vonrhein wrote:
> There is a collection of posts (unfortunately with a number of spam
> messages) at
>
>   http://wwpdb-remediation.rutgers.edu/mail-archive/
>
> with various comments. Although I'm not familiar with the internal
> workings of this remediation program, it seems indeed that the PDB
> format is now largely auto-generated from the internally used
> mmCIF. Unfortunately in my experience (having had a look at a few dozen
> random entries of the new PDB files) this means that some of the new
> PDB files of old entries will look very different from what you/we
> deposited several years ago. The format seems better (internally
> consistent) but the content has sometimes suffered.
>
> But I guess there is always room for frictions when one side is mainly
> interested in data format, storage and databases and the other mainly
> interested in the crystallographic content. Finding a good compromise
> between those two groups of experts is non-trivial.
>
> At least the new databases will always have a link to the original
> version of the PDB file - although it will still mean I can't now
> search for an author name MUELLER (German U-umlaut transfered in the
> proper ASCII format), since the PDB files now contain MULLER (because
> PUBMED isn't able to properly translate non-ASCII names ...). Or an
> analysis of programs used for structure solution will show a veri
> different distribution - since the information has been significantly
> changed.
>
> Anyway, have a look at your favourite PDB file with the attached
> script
>
>   ./pdb23.sh 1abc
>
> It is quite interesting sometimes. I haven't cehcked the mmCIF files -
> maybe they are much better (as a 'hint' from the database people to
> the crystallographers to stop using PDB format and switch to mmCIF,
> maybe?).
>
> Cheers
>
> Clemens
>
> On Sat, Jul 21, 2007 at 12:05:35PM -0700, Ethan A Merritt wrote:
>   
>> On Saturday 21 July 2007 11:12, Joe Krahn wrote:
>>     
>>> we all use in our daily research. They don't even want to keep the PDB
>>> format at all. It's primary purpose now is for structural biologists.
>>>       
>> That is inevitable.  The PDB format is simply not capable of representing
>> the complexities of current crystallographic models, and will only become
>> more obsolete as the state of the art progresses.  Because it is so wide-
>> spread, it will remain a legacy format for import/export into programs 
>> that are not up to the current crystallographic state of the art.  Yes,
>> that means it will largely be used by non-crystallographers to import
>> and view structures.
>>
>> Thus I think the writing is on the wall that the PDB format as a primary
>> working medium in crystallography is on its deathbed.  Of course it may
>> linger there for a long while yet, and may be poked at from time to time
>> in order to stave off its final expiration.
>>
>> Having said that, I don't understand the motivation for changing this
>> legacy format to something that the legacy programs will not recognize.
>> That indeed seems self-defeating.
>>
>> 	Ethan Merritt
>>
>>
>>
>>     
>>> The new PDB format (version 3) has a lot of very useful improvements,
>>> and an update is long overdue. However, I am irate that RCSB chose NOT
>>> to use the ACA meeting to discuss the changes. Instead, the format is
>>> being put into production at the same time as the ACA meeting. It is
>>> essentially stating that opinions expressed at the ACA do not count.
>>> Their was a lot of conflict at their last attempt at an update. Instead
>>> of working to better involve the structural biologist community, I feel
>>> that they are intentionally discounting our interests because working
>>> with the user community is too much effort.
>>>
>>> Unfortunately, structural biologists generally do not want to spend time
>>> arguing about file formats, while computer scientists can carry on for
>>> weeks over minor details. This change is going to affect all of us. If
>>> you have concerns about the new format that have not been addressed, it
>>> is important to take action now. The PDB format is not just their
>>> personal database format (that's what mmCIF is for), but the format that
>>> we all use in our daily research. They don't even want to keep the PDB
>>> format at all. It's primary purpose now is for structural biologists. It
>>> is essential that we be part of the decision making process.
>>>
>>> I just sent the following letter to the wwPDB, which is where
>>> comments about the new format are supposed to go. If you will be at the
>>> ACA meeting, I encourage you to complain loudly.
>>>
>>> Joe Krahn
>>>
>>> -----------------------------------------------------------------------
>>> To: [log in to unmask]
>>> Subject: The new PDB format is WRONG.
>>>
>>> It seems obvious to me that the RCSB and wwPDB worked on the new format
>>> to consider database users needs, but has intentionally ignored the rest
>>> of the user community. RCSB manages mmCIF for database purposes, and has
>>> declared a lack of interest in even keeping the PDB format. Obviously,
>>> the primary purpose of the PDB format is for structural biologists
>>> working with individual structures, and not database users.
>>>
>>> Most of the updates are quite positive and beneficial, but I think that
>>> some changes are detrimental. My only serious complaint is that RCSB,
>>> and now wwPDB, seem to be ignoring the interests of much of the
>>> scientific community which they are supposed to be serving. All that I
>>> ask for is appropriate inclusion of all of the user community. This is a
>>> big change that will affect thousands of people. We should ensure that
>>> it is the best possible format update before we all have to expend a
>>> huge effort to deal with it.
>>>
>>> I have seen many comments about the format by well known
>>> crystallographers ignored. One example is the use of SegID. Most
>>> structural biologists have favored it for years, but RCSB continued to
>>> deny us, on grounds that it is not "well defined". It would be better to
>>> make a better definition, and allow it to be used to group together
>>> non-covalent groups, such as waters with a specific protein molecule.
>>> This is important because the use of ChainID for non-polymers has been
>>> banned, which also goes against the wishes of most users.
>>>
>>> The latest atom alignment rule changes is also detrimental. RCSB has
>>> totally broken the element alignment rules, on baseless grounds that it
>>> was too hard to follow. The new change convolutes this rule even
>>> further, and essentially follows an earlier attempt at IUPAC hydrogen
>>> names that the community strongly rejected. At this point, the best
>>> solution is probably to make it completely left justified. Again, my
>>> main concern is not to follow my idea, but to ensure that the user
>>> community gets a fair chance to participate in the final decision.
>>>
>>> Another problem is that the original meaning of HET groups continues to
>>> be corrupted. ATOM records are for commonly occurring residues from a
>>> list of standard residues. Water is obviously common, and should not
>>> have been converted to a HET group. HET groups have NO relation ship to
>>> polymeric state. With water as a HET group, a proper PDB file for a
>>> modeller with bulk solvent would require CONECT entries for every single
>>> water. It is also important to emphasize that the HETNAM is the actual
>>> unique ID, not the 3-letter code. The current hack is to treat
>>> everything as an ATOM, which has a pre-determined connectivity. This
>>> cannot continue forever, and we are already stuck with meaningless
>>> 3-letter codes instead of useful 3-letter abbreviations. The unique
>>> 3-letter code should be continued for now, but there should be an
>>> emphasis on beginning to use the full HETNAM so that the inevitable
>>> switch top non-unique 3-letter codes will not have a big impact.
>>>
>>> Thank you,
>>> Joe Krahn
>>>
>>>       
>> -- 
>> Ethan A Merritt
>> Biomolecular Structure Center
>> University of Washington, Seattle 98195-7742
>>
>>     
>
>   


-- 
Jeroen Raymundus Mesters, Ph.D.
Institut fuer Biochemie, Universitaet zu Luebeck
Zentrum fuer Medizinische Struktur und Zellbiologie
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Tel: +49-451-5004070, Fax: +49-451-5004068
E-mail: [log in to unmask]
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Http://www.opticryst.org
--
If you can look into the seeds of time and say
which grain will grow and which will not - speak then to me  (Macbeth)
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