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 <[email protected]> Date: 2013/08/05 01:03 (GMT-08:00) To: [email protected] 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-----
