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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: "Herbert J. Bernstein" <yaya@bernstein-plus-sons.com>
- Date: Thu, 22 Mar 2007 15:21:25 -0400
- In-Reply-To: <4602D591.5050005@niehs.nih.gov>
- References: <4602C0BF.3080703@niehs.nih.gov><4602C601.7060308@mcmaster.ca> <4602D591.5050005@niehs.nih.gov>
Methods, e.g. as proposed in DDLm, are more useful than equations. I would suggest working within that context. At 3:14 PM -0400 3/22/07, Joe Krahn wrote: >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 _______________________________________________ imgcif-l mailing list imgcif-l@iucr.org http://scripts.iucr.org/mailman/listinfo/imgcif-l
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- [Imgcif-l] ImgCIF Densiry Maps (Joe Krahn)
- Re: [Imgcif-l] ImgCIF Densiry Maps (David Brown)
- Re: [Imgcif-l] ImgCIF Densiry Maps (Joe Krahn)
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