Re: mmCIF extension dictionary released for review ...

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• Previous message: John Westbrook: "Re: chem_comp"

Hello

John has asked me to post the comments that I made on the technical
presentation of the extension dictionary during the COMCIFS review
phase. Here they are: 

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save__phasing_MIR_der.power_acentric
The meaning of the following phrase is not clear:
"Phasing power is <FH / Lack_of_closure>." 
    - what is FH?
    - what is Lack_of_closure? If a general descriptive phase, the
      underscores may be omitted (cf "Isomorphous difference" in
      save__phasing_MIR_der.R_cullis_acentric). If a single symbolic
      reference, it should be properly defined.
    - do the angle brackets have any meaning (e.g. "expectation value")?
      If not, should they be dropped altogether? Replaced by parentheses?
      Is the placement correct? (i.e. not <FH>/<Lack_of_closure>?)

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save__phasing_MIR_der.R_cullis_acentric
Same comments as above regarding "Lack_of_closure" and angle brackets.

The meaning of this sentence is not clear:
"NB:  This is tabulated for acentric and anomalous terms,
      extending the former definition."
    - what is the former definition? Presumably it is the equation

                           sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
               R~cullis~ = ----------------------------------------
                                   sum|Fph~obs~ - Fp~obs~|

      given in save__phasing_MIR_der_shell.R_cullis, in which case
      reference should be made to the location of this definition.
    - is there a reference to the tabulation for acentric and anomalous
      terms?
    - should the literature reference to the paper of Cullis et al.:
               Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
                    & North, A. C. T. (1961). Proc. R. Soc. A265, 15-38.
      appear in any case?
    - i.e. is the quantity still properly named as a "Cullis R factor"?
Here is a suggested alternative definition:
    _item_description.description
;              Residual factor R~cullis~ for acentric reflections in this
               derivative.

               The Cullis R factor is the ratio of the lack of closure and
               isomorphous difference terms. It is defined in terms of an
               analytical formula for centric reflections, but must be
               extracted or interpolated for acentric and anomalous
               reflections from the tabulation of XXXXX XXXXX XXXXX XXXX.

               Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
                    & North, A. C. T. (1961). Proc. R. Soc. A265, 15-38.
;

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save__phasing_MIR_der.R_cullis_anomalous
The quantity is defined twice:
"Cullis R factor is <Lack_of_closure>/<Isomorphous difference>."
"Cullis  Rfactor is <Lack_of_closure>/<Anomalous difference>"
    - have two definitions been conflated?

I find the nomenclature confusing and not fully explained - what are FPHi(+)
and FPHi(-)? What is FHi"? The various Dano terms? RC(ano) should be
called something else - R~cullis~ or R~cullis~^ano^ perhaps?

Small point - "Sum" in the equation should be "sum" for consistency with
other such expressions.

Is the Cullis et al. literature reference appropriate here too?

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save__phasing_MIR_shell.reflns_anomalous
Doesn't exist - should it? (i.e. there are _centric and _acentric
definitions, but no _anomalous.)

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REFLN_SYS_ABS
Is not this entire category a candidate for the Core dictionary?

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save__refln_sys_abs.index_l
Typo: "Miller index h of the reflection." should of course be "Miller index l
of the reflection."

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save__refine.overall_ESU_B
"Overall estimated standard uncertainties" should be "Overall standard
uncertainty". Presumably this is the quantity sigma_B (the equation gives
(sigma_B)^2).

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save__refine.overall_ESU_ML
Seems identical to the sigma_B definition apart from the numerical factor
(3/8 versus 8). Is this correct?

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save__refine.overall_ESU_R_Cruickshanks_DPI
Better named as "_refine.overall_ESU_R_Cruickshank_DPI" (i.e. without the s
at the end of Cruickshank)?

What does DPI stand for?

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save__refine.overall_ESU_Rfree
better named as "_refine.overall_ESU_R_free" (i.e. with an _ after the R)?

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save__refine.overall_FOM_free_Rset
better named as "_refine.overall_FOM_free_R_set" (i.e. with an _ after the R)?

_item.name is incorrectly given as '_refine.overall_FOM_work_Rset' (and
likewise _item_aliases.alias_name as '_refine.ebi_overall_FOM_work_Rset').

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save__refine.overall_FOM_work_Rset
better named as "_refine.overall_FOM_work_R_set" (i.e. with an _ after the R)?

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save__refine_analyze.RG_d_res_high
refers to "__refine_analyze.ls_RG_free" - typo? Also in 
save__refine_analyze.RG_d_res_low.

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save__refine_analyze.RG_work_free_ratio
would be better as "_refine_analyze.RG_free_work_ratio" (to match the
definition as the free/work ratio).

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save__refine_funct_minimized.numterms
would be better as "save__refine_funct_minimized.number_terms"

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save__refine_ls_restr.type
The new RESTRAIN labels are verbose - not necessarily a problem, though
there may be an implication to a casual user that any old sentence or phrase
could go in here. 

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save__refine_ls_restr.U_sigma_wghts
Should we go for the extra two letters of .U_sigma_weights for clarity?

"The expected r.m.s. differences in thermal parameter, either Uiso or Uaniso,
are listed for each shell in  _refine_ls_restr.ebi_rmsdev_dictionary."
    - _refine_ls_restr.ebi_rmsdev_dictionary is not defined in this batch of
      data names
    - is it a generally useful data name or does it have application only to
      the RESTRAIN program? 
    - the same question might indeed be asked of the .U_sigma_weights
      data name itself.
    - the .ebi_rmsdev_dictionary refers presumably to a tabulation of
      values that are to be regarded as a set of standards characterising
      the particular structure under investigation. This use of the term
      "dictionary" (also used elsewhere in protein structural science
      for standard tabulations, if I am not mistaken) is unfortunate
      within the nomenclature of CIF and its associated data dictionaries.
      Is there a suitable synonym acceptable to the macromolecular community?

"...in both cases, WU is the value stored in _refine_ls_restr.U_sigma_wghts."
    - _refine_ls_restr.U_sigma_wghts (or _weights) is not defined: is this a
      typo for _refine_ls_restr_type.U_sigma_wghts? Likewise the definition
      begins with a reference to refine_ls_restr.ebi_U_sigma_wghts - should
      this be _refine_ls_restr_type.ebi_U_sigma_wghts (note also the missing
      initial underscore)?
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Regards
Brian
_______________________________________________________________________________
Brian McMahon                                             tel: +44 1244 342878
Research and Development Officer                          fax: +44 1244 314888
International Union of Crystallography                  e-mail:  bm@iucr.ac.uk
5 Abbey Square, Chester CH1 2HU, England                         bm@iucr.org
(Coordinating Secretary, COMCIFS)

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