Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

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
  • DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed;d=rcsb-org.20150623.gappssmtp.com; s=20150623;h=subject:to:references:from:message-id:date:user-agent:mime-version:in-reply-to:content-transfer-encoding;bh=4OxzBJ7Hj1PCov3Uxn5x4zs1dbieI0YjFZMxCFlSKXA=;b=TKP/LBWqawPFiWFoDGKOanld42LbXlFHxhwD6subNkxAYtUoV/sDP/UZY4c4F1u1gQaAoCp3l6117TWxu3E6RZeadu72LpmPCbr47nXsiSrv+wLJH0ndqJo3OnqPTmH3YKefixN3MWI6PHwR9gkui4pO49EMSA3UUvE9XkL8dPUAbX4lLy0m4mX2GghfMpp+sQE4+xGTangkqz6EQ6Wc011Lm1JP+wko3vQcpGI2eOQ8jBRNjLFprcVJS369NqY17pusRgKLCguMAxo0aP5B3vbkmDVhfxOWWgBtCvqINRsQ+mIhrfqZ/6tEhdcgcIwts0KeWKltJJ1BUxg5NNNaNQ==
  • In-Reply-To: <CAM+dB2ehdeGTU+_FoeNaEfOMCuGbD+EuTGTntM1MPFmFcmau-g@mail.gmail.com>
  • References: <CAM+dB2ehdeGTU+_FoeNaEfOMCuGbD+EuTGTntM1MPFmFcmau-g@mail.gmail.com>
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. ==
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

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.