Search found 38 matches

by jamesrhester
Tue Oct 11, 2016 8:31 am
Forum: Public input on diffraction data deposition
Topic: Retrieving content from a dataset identified by a DOI
Replies: 1
Views: 3277

Re: Retrieving content from a dataset identified by a DOI

Building on Brian's examples 4 and 6, assume we have the following tools: ⋅  'ManifestMaker': A tool that could examine the individual files in a Zenodo deposit, to produce an overall 'manifest'. This manifest could be as simple as an imgCIF file where the individual images are replaced by...
by jamesrhester
Thu May 08, 2014 7:38 am
Forum: Core CIF review and update
Topic: ATOM TYPE category
Replies: 2
Views: 9446

Re: ATOM TYPE category

Agreed. The integer value is the useful one. Also, as far as I can tell the mmCIF/PDBX dictionary has no equivalent. Now, how do we describe natural abundance? We would seriously complicate the description if we were to have separate types for every isotope in the sample, and then have to describe a...
by jamesrhester
Wed May 07, 2014 7:08 am
Forum: Core CIF review and update
Topic: ATOM TYPE category
Replies: 2
Views: 9446

ATOM TYPE category

This thread is for discussion of the ATOM TYPE category. We need a way to handle different isotopes, which have wildly different scattering lengths for neutrons. I propose simply adding _atom_type_atomic_weight to this category in order to allow description of different isotopes. I note that X-ray l...
by jamesrhester
Wed May 07, 2014 6:01 am
Forum: Core CIF review and update
Topic: ATOM_SITES category
Replies: 0
Views: 3672

ATOM_SITES category

This thread is for discussing updates to the ATOM_SITES category.

On first inspection, the most likely candidate for updating is lengthening the list of solution methods (_atom_sites_solution_*) to account for any recent developments. Anything else?
by jamesrhester
Mon Mar 31, 2014 10:39 pm
Forum: Core CIF review and update
Topic: Non-defined datnames being used in published CIFs
Replies: 1
Views: 4057

Re: Non-defined datnames being used in published CIFs

I agree with the need to keep the definitions usable. I suggest that we start by writing to the program authors requesting a description of the respective datanames. The 'squeeze' datanames might be better developed within this group, and run past the program authors for their comments.
by jamesrhester
Tue Mar 11, 2014 4:31 am
Forum: Core CIF review and update
Topic: ATOM_SITE category
Replies: 0
Views: 3182

ATOM_SITE category

DDL1 version DDLm version A cursory look through the DDL1 category suggests that the _atom_site_constraints and _atom_site_restraints tags have been superseded by the constraints and restraints dictionary and should thus be marked as deprecated. I can see no items that need additional enumerated va...
by jamesrhester
Tue Mar 11, 2014 4:06 am
Forum: Core CIF review and update
Topic: Using the Core CIF Review forum
Replies: 0
Views: 2865

Using the Core CIF Review forum

This forum is intended for discussion and review of the Core CIF dictionaries, including the new DDLm dictionaries. Please endeavour to make the first words in the subject line of your message the CIF category or dataname that you are discussing. Proposed updates to the dictionaries will be availabl...
by jamesrhester
Tue Oct 08, 2013 12:13 am
Forum: CIF Application Programming Interface
Topic: Whitespace in table entries
Replies: 5
Views: 11887

Re: Whitespace in table entries

I have no objection to allowing whitespace only between colon and datavalue. As you note here and elsewhere, it is easy to relax this constraint in the future if necessary.
by jamesrhester
Wed Oct 02, 2013 1:07 am
Forum: CIF Application Programming Interface
Topic: Whitespace in table entries
Replies: 5
Views: 11887

Re: Whitespace in table entries

I agree with John's proposal to allow whitespace around the full colon in tables. As the key is a delimited string, detecting the end of the key is not dependent on an immediately following full colon, and likewise, there is no ambiguity introduced by allowing whitespace after the full colon. I woul...
by jamesrhester
Wed Oct 02, 2013 1:02 am
Forum: CIF Application Programming Interface
Topic: Comments vs. whitespace
Replies: 1
Views: 4139

Re: Comments vs. whitespace

I have no objection to any of these proposals. I think the general rule of thumb would be not to change CIF1 behaviour without good reason, and to be flexible if it does not complicate the parser.