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Re: Fwd: COMCIFS minutes

Dear John,

  You, yourself, identified the conflicting DDLm-isms that need to
revert to DDL2 conventions.  Is there anything else involved?  Let's
not let this drag out for another 3 years.  Let's get your list of
specific conflicts between DDLm and DDL2 on the table and be done with
this.  The entire point of DDLm was to bring methods and the power of
DDL2 to the core dictionary, not to move backwards on the advances you
provided with DDL2, so that we will have DDL2 plus methods = DDLm for
everybody.

  I _must_ move forward immediately with methods for imgCIF.  It would
be rather silly to do that in a way that conflicts with DDL2, because
imgCIF has to inter-operate with mmCIF.  The Eiger detector is being
shipped.  Right now it is mainly just smaller ones, but, in about a
year, there will be nice big Eiger 16M's collecting MX data at several
synchrotrons, including NSLS-II, using the HDF5 version of CBF.  The
XFEL transition to HDF5 is likely to happen even sooner than that.  We
really should try to have settled these mapping issues well before
then, or we are going to end up repeating the data processing
nightmare of conflicting mini-cbf formats that is causing trouble with
protein datasets to this day.  I cannot be sure of the necessary HDF5
<--> CBF mappings being done reliably at multiple synchrotrons and
XFELs and in all the processing programs that will be using CBFlib for
this data without moving at least some of the coordinate mappings and
tree<-->table mappings into methods, so imgCIF has to move up to DDLm
very, very soon, yet has to remain compatible with mmCIF.  A fully
interoperable DDLm-DDL2 mapping would help make this feasible.

  It would really be nice if we could settle this and just concentrate
on producing data.

  Regards,
    Herbert

On Fri, Aug 29, 2014 at 9:12 AM, John Westbrook <jwest@rcsb.rutgers.edu> wrote:
> I suggest we first solve the problem with the translation before making a
> statement
> that requires submission to an incomplete specification.
>
> John
>
>
>
> On 8/29/14, 8:30 AM, Herbert J. Bernstein wrote:
>>
>> But, I thought we agree to ensure the lossless translation of
>> dictionaries between DDL2 and DDLm, so there is no reason not to have
>> DDLm reference dictionaries -- for mmCIF and imgCIF they would be
>> essentially the same as the DDL2 dictionaries.   in fact the only
>> thing that is currently missing on the DDL2 side are the methods.  I
>> suspect we can add them in them in to DDL2 a non-conflicting manner.
>> That would leave only the cleanup on the DDLm side we agreed to to
>> have full interoperability.
>>
>> On Fri, Aug 29, 2014 at 8:10 AM, John Westbrook <jwest@rcsb.rutgers.edu>
>> wrote:
>>>
>>> Hi James,
>>>
>>> I do not believe that we agreed to the following with respect to DDL2 -
>>>
>>> ... It was agreed that any new dictionary submitted for COMCIFS approval
>>> should have a canonical DDLm version. This would not preclude development
>>> of
>>> a dictionary using DDL1, but the reference version upon acceptance would
>>> be
>>> DDLm ...
>>>
>>> Until lossless software translation of dictionaries is possible then I do
>>> not think that this is
>>> a reasonable requirement.
>>>
>>> John
>>>
>>>
>>> On 8/28/14, 9:39 PM, James Hester wrote:
>>>>
>>>>
>>>> Dear COMCIFS,
>>>>
>>>> Please find attached some draft minutes from our meeting in Montreal.
>>>> Would those who were present please check them and advise
>>>> Brian or myself of any errors or omissions.
>>>>
>>>> thanks,
>>>> James.
>>>>
>>>>
>>>> --
>>>> T +61 (02) 9717 9907
>>>> F +61 (02) 9717 3145
>>>> M +61 (04) 0249 4148
>>>>
>>>>
>>>> _______________________________________________
>>>> comcifs mailing list
>>>> comcifs@iucr.org
>>>> http://mailman.iucr.org/mailman/listinfo/comcifs
>>>>
>>>
>>> --
>>>
>>> John Westbrook, Ph.D.
>>> RCSB, Protein Data Bank
>>> Rutgers, The State University of New Jersey
>>> Department of Chemistry and Chemical Biology
>>> 174 Frelinghuysen Rd
>>> Piscataway, NJ 08854-8087
>>> e-mail: jwest@rcsb.rutgers.edu
>>> Ph: (848) 445-4290 Fax: (732) 445-4320
>>> _______________________________________________
>>> comcifs mailing list
>>> comcifs@iucr.org
>>> http://mailman.iucr.org/mailman/listinfo/comcifs
>
>
> --
>
> John Westbrook, Ph.D.
> RCSB, Protein Data Bank
> Rutgers, The State University of New Jersey
> Department of Chemistry and Chemical Biology
> 174 Frelinghuysen Rd
> Piscataway, NJ 08854-8087
> e-mail: jwest@rcsb.rutgers.edu
> Ph: (848) 445-4290 Fax: (732) 445-4320
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