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Re: [ddlm-group] Your thoughts on correct approach for DDLmmodulated structures dictionary GEOM categories

  • To: ddlm-group@iucr.org
  • Subject: Re: [ddlm-group] Your thoughts on correct approach for DDLmmodulated structures dictionary GEOM categories
  • From: "john.westbrook@rcsb.org" <john.westbrook@rcsb.org>
  • Date: Thu, 17 Nov 2016 15:53:28 -0500
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Hi James,
We have needed to move away from the historical symmetry operator convention (op_ttt) aswe more routinely encounter translations that cannot be represented as a single digit.We also had no end of trouble with skew in the numbering of operators between programs.
We now prefer to use alternative nomenclature such as y,x,1-z and/or provide orthogonaltransformation matrices. ==
Regards,
John
On 11/17/16 12:57 AM, James Hester wrote:> Dear DDLm-group,>> I am currently going through the DDLm conversion of the modulated structures dictionary. It goes without saying that it will be> split into a core_cif compatible section and an _audit.schema-using extension dictionary, as numerous categories receive extra keys> due to the extra m1,m2,m3... reflection indices. That in itself is not a problem; however, I have come across the following> "interesting" situation in the GEOM categories, and would like your input into how to resolve this:>> The core cif method of identifying a particular atom site for geometry calculation uses the atom label and a symmetry operator of> the form n_qrs, where n is a symmetry operator and qrs are unit cell translations + 5.  So the key datanames for the list of bonds> (GEOM_BOND category) are atom_labels 1 and 2, and site_symmetry 1 and 2.  The bond length can be calculated using the information> encoded in these keys.>> The DDL1 modulated structures dictionary needs more than three translations, so defines new datanames site_ssg_symmetry 1,2 where> the value might be n_qrstuv (i.e. more translations).  The intention is clearly to replace the original site_symmetry keys with the> site_ssg_symmetry keys, so, strictly speaking, GEOM_BOND et. al. are new categories in the ms CIF dictionary. This is starkly> evident in the dREL for geom_bond.distance from core_cif: it is no longer correct, reflecting the fact that most core cif compatible> software that seeks to (re)calculate geom_bond.distance will fail when presented with a msCIF file.>> We seek a resolution that keeps the dREL correct and minimises the chances of incorrect interpretation of a CIF file.>> I see two alternatives:> (1) Allow dictionaries that operate under a different _audit.schema to replace keys, thereby keeping the same category name for what> is essentially a different category. Any dREL-containing definitions must have the dREL rewritten or removed.>> Advantages: "Very similar" datanames do not need to be renamed. DDLm datanames can match DDL1 datanames as closely as possible> Disadvantages: potential trivial redefinition of many datanames in all affected categories. Sets a precedent for giving different> categories the same name?>> (2) Change the GEOM_ categories to (e.g.) GEOM_SSG categories>> Advantages: Strictly correct, no chance of confusion for _audit.schema non-aware programs (hopefully fewer of these as time goes on)> Disadvantages: Will proliferate datanames?>> I am inclined towards (1) on the grounds that:> (a) Once _audit.schema is declared and checked, it is clear that the CIF software author is aware of MS CIF, including any> redefinitions, so there is little danger of silent software mistakes;> (b) Fundamentally the site_symmetry_ datanames are decomposable into 4 key columns each (symmetry operator, 3 translations).  So MS> CIF is simply adding more key columns, in accordance with how we expect _audit.schema to operate.> (c) We (COMCIFS) can always reserve the right to reject new dictionaries that attempt a category rename.>> Can any of you see a problem with option (1)?>> thanks,> James.>>> --> T +61 (02) 9717 9907> F +61 (02) 9717 3145> M +61 (04) 0249 4148>>> _______________________________________________> ddlm-group mailing list> ddlm-group@iucr.org> http://mailman.iucr.org/cgi-bin/mailman/listinfo/ddlm-group>
-- John Westbrook, Ph.D.RCSB, Protein Data BankRutgers, The State University of New JerseyDepartment of Chemistry and Chemical Biology174 Frelinghuysen RdPiscataway, NJ 08854-8087e-mail: john.westbrook@rcsb.orgPh: (848) 445-4290 Fax: (732) 445-4320_______________________________________________ddlm-group mailing listddlm-group@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/ddlm-group

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