There's definitely a case for working formats, but as we think about improved working binary formats following on from MTZ (maybe based on HDF5 containers), particularly for unmerged data (for example in the DIALS project), it makes sense to use [mm]/[image]/cif definitions where appropriate, for ease of conversion and to reduce confusion. However not all data items that are needed (or are desirable) are currently defined, so there will need to be some extensions. There is a particular problem with multiple lattices (e.g. non-merohedral twins) where a single observation (intensity) may have multiple indices hkl attached to it, and this doesn't fit neatly into a rectangular array without padding.
Phil On 19 Sep 2013, at 12:11, Eugene Krissinel <eugene.krissi...@stfc.ac.uk> wrote: > Completely agree. Perhaps there could be a distinction between working and > deposition formats. They are for different purposes and, therefore, could > differ from each other -- Eugene > > On 19 Sep 2013, at 10:45, Phil Evans wrote: > >> Do you really want to read the whole of a long reflection loop into memory >> rather than parsing it one line at a time (which should be possible once you >> have worked out what is in the file)? That would end up with storing the >> reflection list twice, the memory copy of the input file and the internal >> representation for the program. I do get complaints from people trying to >> run e.g. Pointless with large datasets on 32-bit machines, crashing because >> it runs out of memory >> >> If you imagine someone corresponding to the XDS INTEGRATE.HKL file with 120 >> characters/reflection, then a dataset with 10^7 reflections (not >> outrageously large these days) occupies 1.2e9 bytes, over 1GB, which seems a >> lot to add gratuitously to memory demands even on today's computers >> >> Of course (in my opinion) a working format (as opposed to an archive format) >> should be binary for size, accuracy (FP dynamic range) and speed. >> A quick comparison (using Pointless) >> >> Read 5.3e6 reflections from a formatted XDS INTEGRATE.HKL file, 608MB, 15 >> secs >> Read equivalent binary MTZ file, 262MB, 2.6 secs >> >> Phil >> >> On 18 Sep 2013, at 15:58, yayahjb <yaya...@gmail.com> wrote: >> >>> Dear Colleagues, >>> >>> There are two major issues that tend to trip up CIF programmers: >>> >>> 1. Dealing with the order independence of CIF. Unlike PDB format, tags in >>> CIF can validly >>> be presented in any order. This means you cannot simply scan a CIF for a >>> tag you want and >>> start processing from that point forward as you do with a PDB file. In >>> general to read >>> a CIF properly, you need to read all of it into memory before you can do >>> anything with it. >>> A common mistake is to assume that just because many CIFs have been written >>> with tags in >>> a given order, the next CIF you encounter will also have the tags in that >>> order. >>> >>> 2. Doing the lexical scan (the tokenizing) correctly. CIF uses a context >>> sensitive grammar, >>> so lexers based on simple BNF tend to make mistakes, and most reliable CIF >>> lexers are >>> hand-written rather than being generated from a grammar. The advice to use >>> a pre-written >>> and tested lexer is sensible. >>> >>> The bottom line is that, while it is relatively easy to write a valid CIF, >>> reading CIFs reliably >>> can be a very challenging programming task, because you need to write code >>> that will handle >>> the very complex general case, rather than just specific examples. >>> Fortunately there are >>> software packages to help you do this. >>> >>> Herbert J. Bernstein >>> >>> On 9/18/13 10:41 AM, Peter Keller wrote: >>>> Hi Phil, >>>> >>>> I agree that the issue that you raise (about the need to define the data >>>> items and categories propery) is an important one that needs proper >>>> consideration. However, your mail could be read to suggest that correct >>>> parsing of CIF-format data is a secondary issue that doesn't deserve the >>>> same attention from developers. >>>> >>>> I hope that this isn't quite what you meant.... There are already >>>> mutually-incompatible CIF dialects out there that have been created by >>>> developers coding to their own understanding and interpretations of the >>>> CIF/STAR format. I am sure that you would not want to be the creator of >>>> yet another one :-) Correct tokenising is a necessary (but not sufficient) >>>> condition for preventing the problem getting worse. >>>> >>>> In practice, the code and applications that I have seen, and the >>>> discussions about this that I have had, all suggest that developers find >>>> it more difficult to write code that tokenises CIF/STAR-format data >>>> correctly than code that handles other text formats that they have to deal >>>> with in this field. My experience suggests that this is an important >>>> practical issue with real-world ramifications, and it is worthwhile >>>> devoting some effort to it. >>>> >>>> Regards, >>>> Peter. >>>> >>>> On Wed, 18 Sep 2013, Phil Evans wrote: >>>> >>>>> Date: Wed, 18 Sep 2013 13:38:07 +0100 >>>>> From: Phil Evans <p...@mrc-lmb.cam.ac.uk> >>>>> To: CCP4BB@JISCMAIL.AC.UK >>>>> 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 <pkel...@globalphasing.com> 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 >>>>> >>>> > > > -- > Scanned by iCritical. >
