I just hope that one day we all will be discussing a sort of universal API to read/write structural information instead of referencing to raw formats, and routines to query MX data, which would be more appropriate than grep (would many SB students/postdocs use grep these days? but many if them would need to inspect files somehow). This, in essence, is similar to discussing read/write primitives in C/C++/Fortran rather than I/O functions of BIOS and HDD/BUS commands that they drive.
No format can suite everybody, especially given the complexity of macromolecular data. In contrary to the conspiracy theory of Tim, transition to mmCIF is actually driven by scientists, rather than programmers. PDB has limitations (e.g. limits on the number of atoms, residues and chains), which make it not suitable in many cases today and definitely not for future. This has been discussed many times, and one has to take measures one day; seems like that day is coming. But I would really like to accentuate that working with raw format, whether through grep or otherwise, should increasingly become more and more unnecessary habit, to say the least. Formats will evolve whatever happens, and the only proper way to cope with it as a moving target is to use a maintained API. Eugene On 5 Aug 2013, at 11:10, kaiser wrote: Tim, Having not read Gerard Kleywegt's announcement, and not considering myself a programmer, I have to disagree with the majority of your statement. Yes, using grep on mmcif files is "awk"ward (but petfectly possible); awk on the other hand works much better. It's actually more of a pain to use it on pdb files. And perl, well perl can handle anything and it will always look nice while you write it and never look nice when you look back at it... Just my 2 cents, Jens Sent from my T-Mobile 4G LTE Device -------- Original message -------- From: Tim Gruene <t...@shelx.uni-ac.gwdg.de<mailto:t...@shelx.uni-ac.gwdg.de>> Date: 2013/08/05 01:03 (GMT-08:00) To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] mmCIF as working format? -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, having read Gerard Kleywegt's latest announcement on the wwPDB Workshop (1st August) made me wonder whether it is planned to introduce mmCIF as working format to users in addition to using it at e.g. the PDB, because I think that would make life unnecessarily complicated. The example mmCIF file for GroEL is about 7.5 times bigger than its PDB file. I know that disk space is 'cheap' nowadays, but that does not make it fast. And personally I find mmCIF very awkward to work with, since it is not line-oriented. 'grep', 'awk', 'perl' etc. do not work well on XML-like files. Instead of using mmCIF, one could, e.g. introduce a free format PDB format, with space holders for non-assigned entities, and maybe a line continuation character. If mmCIF is not going to be the working format for MX (refinement) programs I would be happy for a reassurance, and otherwise I would appreciate some comments about the benefits of an XML file format over a line-oriented free format for the scientists that work with structural data. I my opinion, using XML (or mmCIF) for structural information is an attempt of programmers to make themselves more indespensable to scientists, rather than scientifically needed. Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.14 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFR/1xbUxlJ7aRr7hoRAkLNAKClH9RpAA7NJsH3YFOTguOo9kjwoQCZAf/m JF1oyJNuq+8b+VsywDupElo= =bvb3 -----END PGP SIGNATURE----- -- Scanned by iCritical.
