As a novice looking at mmCIF from a developers point of view, for reflection data, the complication is not so much tokenising (parsing), but what items to write or to expect to read. For example as far as I can see an observed intensity may be encoded in a reflection loop (merged or unmerged) as any one of the following, and there seem to be similar choices for other items:-

 
_refln_intensity_meas
_refln.F_squared_meas
_refln.pdbx_I_plus, _refln.pdbx_I_minus

_diffrn_refln.counts_net
_diffrn_refln.intensity_net

If I'm writing a file, which should I use, and if I'm reading one which ones should I expect? And is there a distinction between merged and unmerged data?

confused (easily)
Phil



On 17 Sep 2013, at 15:30, Peter Keller <[log in to unmask]> wrote:

> Dear all,
> 
> At Global Phasing, we have seen that there are still issues with the way that different applications deal with mmCIF-format data, and this continues to cause problems for users. I believe that part of the reason for this is that the underlying syntax (the STAR format) is not universally understood, and that a common and complete understanding of the full STAR syntax amongst programmers who deal with the format will help with some of the existing problems.
> 
> I wrote some code for low-level handling of the STAR format a while ago that I have been meaning to release for over a year. Garry Battle's announcement on 23 August about the mmCIF/PDBx workshop at the EBI has prompted me into action: I have written a short article that discusses some examples of the issues that we have encountered, and made my code available for download. The references in the article are given primarily as web links: more conventional citations can usually be found in the pages that I link to. This code has not been used in any released products, but it has had some internal use at Global Phasing. There is an MX bias in the article's discussion, but the issues are not restricted to MX.
> 
> As I explain in the article, the handling of the input data is based on an enourmous regular expression that matches STAR data, with only a little logic in the code itself. The regular expression should be usable with a variety of other languages, not only in Java (which I have used in this case). The code, or the regular expression on its own, may be freely used in other projects: see the included licencing for details, but basically you should: (i) give credit for using it, and (ii) if you choose to modify the regular expression, state that you have done so in that credit.
> 
> The article, which contains links to a tar file containing the code, and the documentation, is here:
> 
>   <http://www.globalphasing.com/startools/>
> 
> Hoping that others will find this useful and/or help to resolve or clarify outstanding questions,
> 
> Peter.
> 
> -- 
> Peter Keller                                     Tel.: +44 (0)1223 353033
> Global Phasing Ltd.,                             Fax.: +44 (0)1223 366889
> Sheraton House,
> Castle Park,
> Cambridge CB3 0AX
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