 |
 |
Hi Phil, When I wrote cif2cif to deal with reflection files from the PDB I opted for good-enough parsing to provide input for cif2mtz. This was a while ago, reflection files were still a mess at the time and my programming skills never tested in practice. I just added support for anything that could be (merged) F's or I's and all the variations found by mining the reflection files of the PDB. I treated things like _refln.intensity_meas and _refln.F_squared_meas as equivalent because they never seemed to occur together in the same file anyway. A more elegant approach would be to expect anything (or at least be able to ignore the things you do not support), and then just find the column you actually want, or move through a hierarchy of similar things. You can then treat the data and write it out in what you think is the most appropriate type. For compatibility reasons, I would try to stick to data columns that are common. E.g. PDB seems to like _refln.F_meas_au and _refln.intensity_meas which also means that most other programs that deal with mmCIF reflection files support that. I guess checking with the developers of cif_to_mtz converters of the different software packages is the way to go. Cheers, Robbie (who needs to look at adding support for unmerged data) > -----Original Message----- > From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of > Phil Evans > Sent: Wednesday, September 18, 2013 14:38 > To: [log in to unmask] > Subject: Re: [ccp4bb] Code to handle the syntax of (mm)CIF data correctly. > > 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 > > United Kingdom