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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 19:04:45 -0400
- In-Reply-To: <4602D9C8.6020106@mcmaster.ca>
- References: <4602C0BF.3080703@niehs.nih.gov><4602C601.7060308@mcmaster.ca> <4602D591.5050005@niehs.nih.gov><4602D9C8.6020106@mcmaster.ca>
David Brown wrote: > Joe Krahn wrote: > >> 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. >> > The Hall symbol is a space group name (symbol) that specifies all > possible settings of the 230 regular space groups. It can easily be > expanded into the list of the expressions of symmetry operations. > >> 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. >> > This would be useful. I assume that the existing format could be > extended using notation such as x/72,y-56/72 etc. CIF does have > definitions for symmetry operations in higher dimensions, but not, I > believe, for non-crystallographic symmetries > I actually meant for the virus example to be one where the equation form is not an advantage. So, even though it is a simple concise method, it is not always applicable, and the simple matrix+vector might be better as a general form. And, I suspect most people would prefer to minimize variations. For comparison, mmCIF allows either the Hall symbol or explicit symmetry operators. In the latter case, they are in equation form: mmCIF already defines symm-ops as equations: _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z 2 -x,-y,-z 3 -x,1/2+y,1/2-z 4 x,1/2-y,1/2+z NCS is also part of mmCIF, with matrix+vector, like this: _struct_ncs_oper.matrix[1][1] 0.247 _struct_ncs_oper.matrix[1][2] 0.935 _struct_ncs_oper.matrix[1][3] 0.256 _struct_ncs_oper.matrix[2][1] 0.929 _struct_ncs_oper.matrix[2][2] 0.153 _struct_ncs_oper.matrix[2][3] 0.337 _struct_ncs_oper.matrix[3][1] 0.276 _struct_ncs_oper.matrix[3][2] 0.321 _struct_ncs_oper.matrix[3][3] -0.906 _struct_ncs_oper.vector[1] -8.253 _struct_ncs_oper.vector[2] -11.743 _struct_ncs_oper.vector[3] -1.782 Joe _______________________________________________ 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)
- Re: [Imgcif-l] ImgCIF Densiry Maps (David Brown)
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