Re: [Jmol-users] Bye Bye mmCIF?
On Sun, Apr 22, 2012 at 10:40 PM, Eric Martz ema...@microbio.umass.edu wrote: This is the first I've heard about PWF. There are some slides by Helen Berman about it here: http://www.rcsb.org/pdb/general_information/about_pdb/rcsbpdbac10-presentations.pdf Listening to a talk from Gerard Kleywegt (PDBe) right now, who just said the wwPDB is in fact based on mmCIF (with PDBx)... I asked about a draft specification, and he mentioned they are working on a website, but had no further detail... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bye Bye mmCIF?
I would encourage programmers to continue to write mmCIF readers, at least, since this will continue to define the exchange of full data sets from the PDB. Hence, IUCr journals will import data from the PDB in mmCIF format, since that will contain all the information associated with a deposition that could also be used in the journal. An example of this is the IUCr journals' toolkit for creating enhanced figures using Jmol - the toolkit automatically fetches the mmCIF from the Protein Data Bank. Many applications, of course, won't use most of the additional information in an mmCIF, and just need a fast (and robust) way to input 3-d positional coordinates. But it's actually not difficult to write a routine to do that from an mmCIF, and, once the lexical scanning and parser functionality have been fine-tuned (and they're not fundamentally different from core CIF), your application can just skip over the mmCIF contents that aren't considered relevant. There *are* software libraries that might help (http://www.iucr.org/resources/cif/software), although in honesty several of these are rather heavyweight. But if your application already has a core CIF reader, extension to use mmCIF in a pragmatic way probably won't be that difficult. The *ideal* (and Jmol, as usual, already is ideal in this respect!) is to provide hooks within your application that can pass arbitrary mmCIF content to another application, even if you don't make any further use of it yourself. Thus Jmol can sit conveniently in the middle of a software workflow that might be using all the richness of a fully populated mmCIF data set. I haven't studied the details of PWF yet, but you'll see that it is structured in such a way that it's likely to be readable with relatively few tweaks to an existing mmCIF reader anyway. Best wishes Brian _ Brian McMahon tel: +44 1244 342878 Research and Development Officerfax: +44 1244 314888 International Union of Crystallographye-mail: b...@iucr.org 5 Abbey Square, Chester CH1 2HU, England On Sun, Apr 22, 2012 at 04:40:25PM -0400, Eric Martz wrote: This is the first I've heard about PWF. There are some slides by Helen Berman about it here: http://www.rcsb.org/pdb/general_information/about_pdb/rcsbpdbac10-presentations.pdf Eric At 4/21/12, you wrote: Content-Language: en-US Content-Type: multipart/alternative; boundary=_000_DA18B365B7F24FEBAC31246EE3E79B03weizmannacil_ Maybe we don't need to invest too much on mmCIF support, and concentrate on the upcoming PWF (wwPDB Working Format). This might be the new format that (based on an undisclosed source), PDB is seeking to get the crystallographic community approval on. When, how and if this will happen is unknown to me. Jaim On Apr 21, 2012, at 3:41 PM, Kevin Theisen wrote: Hi Bob, It appears FF4 is mmCIF, which we do not support (at least not yet). I will have to do some more study of the CIF format to make sure I understand why there are so many variations, but currently, if your file matches the core CIF spec, then it will load without issue: http://it.iucr.org/G/http://it.iucr.org/G/ Bests, Kevin -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Bye Bye mmCIF?
This is the first I've heard about PWF. There are some slides by Helen Berman about it here: http://www.rcsb.org/pdb/general_information/about_pdb/rcsbpdbac10-presentations.pdf Eric At 4/21/12, you wrote: Content-Language: en-US Content-Type: multipart/alternative; boundary=_000_DA18B365B7F24FEBAC31246EE3E79B03weizmannacil_ Maybe we don't need to invest too much on mmCIF support, and concentrate on the upcoming PWF (wwPDB Working Format). This might be the new format that (based on an undisclosed source), PDB is seeking to get the crystallographic community approval on. When, how and if this will happen is unknown to me. Jaim On Apr 21, 2012, at 3:41 PM, Kevin Theisen wrote: Hi Bob, It appears FF4 is mmCIF, which we do not support (at least not yet). I will have to do some more study of the CIF format to make sure I understand why there are so many variations, but currently, if your file matches the core CIF spec, then it will load without issue: http://it.iucr.org/G/http://it.iucr.org/G/ Bests, Kevin -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Bye Bye mmCIF?
Maybe we don't need to invest too much on mmCIF support, and concentrate on the upcoming PWF (wwPDB Working Format). This might be the new format that (based on an undisclosed source), PDB is seeking to get the crystallographic community approval on. When, how and if this will happen is unknown to me. Jaim On Apr 21, 2012, at 3:41 PM, Kevin Theisen wrote: Hi Bob, It appears FF4 is mmCIF, which we do not support (at least not yet). I will have to do some more study of the CIF format to make sure I understand why there are so many variations, but currently, if your file matches the core CIF spec, then it will load without issue: http://it.iucr.org/G/ Bests, Kevin -- For Developers, A Lot Can Happen In A Second. Boundary is the first to Know...and Tell You. Monitor Your Applications in Ultra-Fine Resolution. Try it FREE! http://p.sf.net/sfu/Boundary-d2dvs2___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
