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Item 5.2

  • To: Multiple recipients of list <coredmg@iucr.org>
  • Subject: Item 5.2
  • From: "I. David Brown" <idbrown@mcmail.cis.mcmaster.ca>
  • Date: Tue, 18 Jun 2002 16:57:41 +0100 (BST)
Dear Kathleen,

	Thanks for your email which I have copied at the end of this
message.  I am also copying this reply to the Core DMG so you will
probably get this message twice.

	Re agenda item 5.2, I note that you feel it is better to stay with
the peptide sequence code already in use when writing CSD entries in CIF,
rather than adopt a new code which would be directly compatible with the
mmCIF descriptions.  I can understand the reasons for this decision and,
as long as your peptide sequence synonym is parseable, as it clearly is, a
conversion to mmCIF should presumably be possible.

	You suggest _CSD_peptide_name or _CSD_peptide_code as the name for
this item.  You mention that there is a CCDC reserved CIF name which
allows you to invent any CIF name that start with _CCDC, but that this
code is used for internal purposes rather than for the items in the
database itself.  The code _CSD has not yet been reserved, but there is no
reason why CCDC should not reserve it for use in transcribing entries in
the database.  There is a list of reserved codes on the IUCr web site
(look under CIF, specification, reserve datanames) and a form for
registering new codes.  I would recommend that CCDC register _CSD for use
when transcribing specialized items from CSD entries into CIF.

	If you do this we can strike item 5.2 from the agenda of the Core

			Best wishes


Dr.I.David Brown,  Professor Emeritus
Brockhouse Institute for Materials Research,
McMaster University, Hamilton, Ontario, Canada
Tel: 1-(905)-525-9140 ext 24710
Fax: 1-(905)-521-2773

On Tue, 18 Jun 2002, Kathleen Foreman wrote:

>  Dear David
>  Your recent report states:
>  "5.2(w) CCDC have also identified a need to include peptide
>  sequences for some of their polypeptides.  They are currently
>  working on a scheme compatible with mmCIF for including this
>  information.  Discussion on this topic should be deferred until
>  we receive their report."
>  We have been considering the possibilities open to
>  us to code the small peptide listings which appear
>  in our database which are particular to the CSD
>  entry. Currently they appear as a compound synonym representing the
>  structure, indicating modifications and linkages,
>  rather than a true peptide sequence.  We have concluded
>  that no advantage can be gained in following the mmCIF
>  model.
>  A typical and simple example is:
>  as defined in my previous email.  However, we include a number
>  of non-standard (modified) amino acids, and have a number of
>  other special symbols to cater for specific situations. We have
>  software modules in ConQuest that permit quite detailed searches
>  of PEPSEQ by our users.
>  It is therefore better if the CSD PEPSEQ information IS regarded
>  as a special sort of structured synonym name, rather than anything
>  else.
>  This seems to point to a special _CSD item for such a
>  text item as opposed to a _ccdc item, as such prefixed
>  fields are currently used for data items not exported
>  from the CSD via CIF.
>  Is there any scope for introducing a _CSD_peptide_code?,
>  or _CSD_peptide_name? or such like?
>  '_citation_journal_id_CSD' is the only specified CSD
>  item at present
> Best wishes
> Kathleen

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