You may want to form you own opinion and take a look at this thread and others in CCP4
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;8e513bea.1308 I hope the link works. There has been extensive and heated debate over the merits of mmCIF vs. PDB on the same BB. The wwPDB is pushing mmCIF, which was developed as an ARCHIVAL format, but in my opinion the community as a whole is rather reluctant to accept mmCIF as a WORKING format. The distinction between a working and archiving format is vital in this context. As far as I am concerned the PDB format as a working format is unmatched in its utility (try to concatenate 2 structures in both formats or prepare a file for MR and you see what I mean), but has drawbacks, some of which would be adapted by an extended PDB format. So as long as the current programs support PDB, I really could care less what the wwPDB thinks; however if programs drop support for the PDB format, I'll be more than happy to look for alternatives... Cheers, Carsten -----Original Message----- From: Albert [mailto:mailmd2...@gmail.com] Sent: Sunday, November 22, 2015 2:23 PM To: Thomas Holder Cc: pymol-users Subject: Re: [PyMOL] default fetch format Hi Thomas: thanks a lot for helpful advice. May I ask is there any superior features of mmCIF format against PDB format? regards Albert On 11/22/2015 04:15 PM, Thomas Holder wrote: > Hi Albert, > > Unfortunately the default fetch type can't be configured. But you can > override the fetch command. Example which you could place in your ~/.pymolrc > file: > > python > from pymol import cmd > > def fetchpdb(*args, **kwargs): > if 'type' not in kwargs: > kwargs['type'] = 'pdb' > return cmd.fetch(*args, **kwargs) > > cmd.extend('fetch', fetchpdb) > python end > > However, if you don't have a compelling reason to work with PDB instead of > mmCIF, then I recommend to give the new mmCIF default a try. > > Cheers, ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Go from Idea to Many App Stores Faster with Intel(R) XDK Give your users amazing mobile app experiences with Intel(R) XDK. Use one codebase in this all-in-one HTML5 development environment. Design, debug & build mobile apps & 2D/3D high-impact games for multiple OSs. http://pubads.g.doubleclick.net/gampad/clk?id=254741551&iu=/4140 _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
