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Re: [Imgcif-l] ImgCIF Densiry Maps
- To: The Crystallographic Binary File and its imgCIF application to image data <imgcif-l@iucr.org>
- Subject: Re: [Imgcif-l] ImgCIF Densiry Maps
- From: Joe Krahn <krahn@niehs.nih.gov>
- Date: Thu, 22 Mar 2007 15:14:25 -0400
- In-Reply-To: <4602C601.7060308@mcmaster.ca>
- References: <4602C0BF.3080703@niehs.nih.gov> <4602C601.7060308@mcmaster.ca>
David Brown wrote: > > > Joe Krahn wrote: > >> How many people are working on the new electron-density dictionary? >> > The electron density dictionary is part of the corpus of approved CIF > dictionaries, but it is designed to report accurate electron density > measurement on small cell crystals using atom-centered multipole > functions. I suspect you are looking for lower resolution elelctron > density maps of protein molecules and I am not aware of any group > working on a CIF representation of that. I had written to Herbert a few weeks back and said "Shouldn't there be a CIF electron-density map specification?", to which he replied that such a thing had just recently been discussed. I suspect he was referring to the current hi-res density specification. In any case, it would be good to incorporate low-res maps as well. > >> >> So, matrix/vector symmetry should be supported. Are there opinions as to >> whether the equation method should or should not also be supported for >> things like electron-density maps? >> > Dictionaries defined using DDLm (previously DDL3) allow matrices and > vectors to be reported as a single item. It is the awkwardness of the > presentation of matrices in DDL1 and DDL2 dictionaries that discouraged > us from defining a matrix+vector representation of symmetry operations > in the current suite of dictionaries. CIF also supports the use of the > Hall space group symbol which uniquely defines the space group > operations, hence the space group and its setting. It is thus more > informative than the Hermann-Mauguin symbol which does not uniquely > specify the origin. > What about equation forms? It is important to define more than just the space group, because non-standard settings can be useful in some cases. It is also useful to include matrix+vector for such things as a spherical asymmetric unit from a 72-fold symmetric virus map. If nobody is working on it, maybe I should go ahead and write down a few alternatives and check opinions of other macro-molecular crystallographers. Thanks, Joe Krahn _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
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