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mmCIF extension dictionary
- To: Multiple recipients of list <comcifs-l@iucr.org>
- Subject: mmCIF extension dictionary
- From: John Westbrook <jwest@ndb.rutgers.edu>
- Date: Fri, 30 Jul 1999 16:43:37 +0100 (BST)
Dear Colleagues,
Please find the following summary of the actions taken in response to
those issues raised in the technical review of the mmCIF extension
dictionary. We are also attaching a copy of the final set of
definitions, and we request that these be approved for incorporation
into the mmCIF dictionary version 2.0.
Best regards,
Paula Fitzgerald
Helen Berman
John Westbrook
---------------------------------------------
Summary of mmCIF extension dictionary issues:
---------------------------------------------
D83.3 mmCIF dictionary extension
--------------------------------
******************************************************************************
David Brown's many comments and technical corrections seems to have been
adequately reponded to by Brian, both in his comments to the list and in
his editting of the draft dictionary. They will not be dealt with further
in this response.
We will, though, respond to each of Brian's comments, as follows.
******************************************************************************
------------------------------------------------------------------------------
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>?)
------------------------------------------------------------------------------
******************************************************************************
The phrase <FH / Lack_of_closure> is a shorthand for the formal expression
of phasing power that is given in the equation that follows it. Since
the shorthand version seems to be causing confusion, and since we
don't carry it in the other data items concerning phasing power in the
main mmCIF dictionary, it is perhaps easiest to just delete it here.
This has been done
******************************************************************************
------------------------------------------------------------------------------
save__phasing_MIR_der.R_cullis_acentric
Same comments as above regarding "Lack_of_closure" and angle brackets.
------------------------------------------------------------------------------
******************************************************************************
Same action - it is gone.
******************************************************************************
------------------------------------------------------------------------------
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.
;
------------------------------------------------------------------------------
******************************************************************************
How about the following - a bit of Brian's expanded definition, and the
equation and reference pulled from the main mmCIF dictionary:
_item_description.description
; Residual factor R~cullis~ for acentric reflections in this
derivative.
The Cullis R factor was originally defined only for centric
reflections. It is, however, also a useful statistical
measure for acentric reflections, which is how it is used in
this data item.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure factor amplitude of the native
Fph~obs~ = the observed structure factor amplitude of the
derivative
Fh~calc~ = the calculated structure factor amplitude from the
heavy atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38.
******************************************************************************
------------------------------------------------------------------------------
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?
------------------------------------------------------------------------------
******************************************************************************
The definition for this data item has been completely revised. If we have
done a good job, all should be clear now.
******************************************************************************
------------------------------------------------------------------------------
save__phasing_MIR_shell.reflns_anomalous
Doesn't exist - should it? (i.e. there are _centric and _acentric
definitions, but no _anomalous.)
------------------------------------------------------------------------------
******************************************************************************
This data item has been added.
******************************************************************************
------------------------------------------------------------------------------
REFLN_SYS_ABS
Is not this entire category a candidate for the Core dictionary?
------------------------------------------------------------------------------
******************************************************************************
We would have no objection to that.
******************************************************************************
------------------------------------------------------------------------------
save__refln_sys_abs.index_l
Typo: "Miller index h of the reflection." should of course be "Miller index l
of the reflection."
------------------------------------------------------------------------------
******************************************************************************
Yes, and you have already fixed that.
******************************************************************************
------------------------------------------------------------------------------
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).
------------------------------------------------------------------------------
******************************************************************************
According to Kim Henrick, the program from which he is harvesting data
outputs (sigma_B)^2, ergo I have modified the definition to refer to
(sigma_b)^2.
******************************************************************************
------------------------------------------------------------------------------
save__refine.overall_ESU_ML
Seems identical to the sigma_B definition apart from the numerical factor
(3/8 versus 8). Is this correct?
------------------------------------------------------------------------------
******************************************************************************
The definition have been modified to refer to (sigma_U)^2.
No, the term ESU_B reflects uncertainty in the thermal parameters, while
ESU_ML reflects uncertainty in the coordinates. ESU_B has 8 and s^4
while ESU_ML has 3/(8 * pi^2) and s^2.
Also, the definition has been modified to refer to (sigma_U)^2.
****************************************************************************2*
------------------------------------------------------------------------------
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?
------------------------------------------------------------------------------
******************************************************************************
DPI stands for Dipsersion Precision Indicator, a measure of error developed
by Cruikshank. The definition has been modified to make this clear.
******************************************************************************
------------------------------------------------------------------------------
save__refine.overall_ESU_Rfree
better named as "_refine.overall_ESU_R_free" (i.e. with an _ after the R)?
------------------------------------------------------------------------------
******************************************************************************
Fine, and you have already make that change.
******************************************************************************
------------------------------------------------------------------------------
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').
------------------------------------------------------------------------------
******************************************************************************
Yes, and you have already fixed the one and changed the other.
******************************************************************************
------------------------------------------------------------------------------
save__refine.overall_FOM_work_Rset
better named as "_refine.overall_FOM_work_R_set" (i.e. with an _ after the R)?
------------------------------------------------------------------------------
******************************************************************************
Fine, and you have already make that change.
******************************************************************************
------------------------------------------------------------------------------
save__refine_analyze.RG_d_res_high
refers to "__refine_analyze.ls_RG_free" - typo? Also in
save__refine_analyze.RG_d_res_low.
------------------------------------------------------------------------------
******************************************************************************
Yes, and you have already fixed both.
******************************************************************************
------------------------------------------------------------------------------
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).
------------------------------------------------------------------------------
******************************************************************************
Yes, and I have also reworded the definition to emphasis the ratio.
******************************************************************************
------------------------------------------------------------------------------
save__refine_funct_minimized.numterms
would be better as "save__refine_funct_minimized.number_terms"
------------------------------------------------------------------------------
******************************************************************************
Fine, and you have already make that change.
******************************************************************************
------------------------------------------------------------------------------
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.
------------------------------------------------------------------------------
******************************************************************************
I take your point, but really these labels are intended to be in the nature
of enumerations, without actually *being* enumerations, as is discussed in
the defintion. It is not inteded that the user would be adding to the
list.
******************************************************************************
------------------------------------------------------------------------------
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)?
------------------------------------------------------------------------------
******************************************************************************
In consultation with Kim Henrick, this data item has been deleted.
******************************************************************************
--------------------------
mmCIF Extension Dictionary
--------------------------
data_cif_mm.dic-ext-v4
#################
## PHASING_MIR ##
#################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save__phasing_MIR.d_res_high
_item_description.description
; The highest resolution in angstroms for the interplanar spacing
in the reflection data used for the native data set. This is
the smallest d value.
;
_item.name '_phasing_MIR.d_res_high'
_item.category_id phasing_MIR
_item.mandatory_code yes
_item_aliases.alias_name '_phasing_MIR.ebi_d_res_high'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR.d_res_low
_item_description.description
; The lowest resolution in angstroms for the interplanar spacing
in the reflection data used for the native data set. This is
the largest d value.
;
_item.name '_phasing_MIR.d_res_low'
_item.category_id phasing_MIR
_item.mandatory_code yes
_item_aliases.alias_name '_phasing_MIR.ebi_d_res_low'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__phasing_MIR.fom
_item_description.description
; The mean value of the figure of merit m for all reflections
phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR.fom'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_fom'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR.fom_acentric
_item_description.description
; The mean value of the figure of merit m for the acentric
reflections phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR.fom_acentric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_fom_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR.fom_centric
_item_description.description
; The mean value of the figure of merit m for the centric
reflections phased in the native data set.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR.fom_centric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_fom_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR.reflns
_item_description.description
; The total number of reflections phased in the native data set.
;
_item.name '_phasing_MIR.reflns'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR.reflns_acentric
_item_description.description
; The number of acentric reflections phased in the native data
set.
;
_item.name '_phasing_MIR.reflns_acentric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR.reflns_centric
_item_description.description
; The number of centric reflections phased in the native data
set.
;
_item.name '_phasing_MIR.reflns_centric'
_item.category_id phasing_MIR
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR.ebi_reflns_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR.reflns_criterion
_item_description.description
; Criterion used to limit the reflections used in the phasing
calculations.
;
_item.name '_phasing_MIR.reflns_criterion'
_item.category_id phasing_MIR
_item_aliases.alias_name '_phasing_MIR.ebi_reflns_criteria'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item.mandatory_code no
_item_type.code text
_item_examples.case '> 4 \s(I)'
save_
#####################
## PHASING_MIR_DER ##
#####################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save__phasing_MIR_der.power_acentric
_item_description.description
; The mean phasing power P for acentric reflections in this
derivative.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure factor amplitude of this
derivative
Fph~calc~ = the calculated structure factor amplitude of this
derivative
Fh~calc~ = the calculated structure factor amplitude from the
heavy atom model
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_der.power_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_power_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.power_centric
_item_description.description
; The mean phasing power P for centric reflections in this
derivative.
sum|Fh~calc~^2^|
P = (----------------------------)^1/2^
sum|Fph~obs~ - Fph~calc~|^2^
Fph~obs~ = the observed structure factor amplitude of the
derivative
Fph~calc~ = the calculated structure factor amplitude of the
derivative
Fh~calc~ = the calculated structure factor amplitude from the
heavy atom model
sum is taken over the specified reflections
;
_item.name '_phasing_MIR_der.power_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_power_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.R_cullis_acentric
_item_description.description
; Residual factor R~cullis,acen~ for acentric reflections in this
derivative.
The Cullis R factor was originally defined only for centric
reflections. It is, however, also a useful statistical
measure for acentric reflections, which is how it is used in
this data item.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis,acen~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure factor amplitude of the native
Fph~obs~ = the observed structure factor amplitude of the
derivative
Fh~calc~ = the calculated structure factor amplitude from the
heavy atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38.
;
_item.name '_phasing_MIR_der.R_cullis_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.R_cullis_anomalous
_item_description.description
; Residual factor R~cullis,ano~ for anomalous reflections in this
derivative.
The Cullis R factor was originally defined only for centric
reflections. It is, however, also a useful statistical
measure for anomalous reflections, which is how it is used in
this data item.
This is tabulated for acentric terms. Any value <1.0 means
there is some contribution to the phasing from the anomalous
data.
sum| |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~| |
R~cullis,ano~ = ---------------------------------------------------
sum|Fph+~obs~ - Fph-~obs~|
Fph+~obs~ = the observed positive Friedel structure factor
amplitude for the derivative
Fph-~obs~ = the observed negative Friedel structure factor
amplitude for the derivative
Fh+~calc~ = the calculated postitive Friedel structure factor
amplitude from the heavy atom model
Fh-~calc~ = the calculated negative Friedel structure factor
amplitude from the heavy atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38.
;
_item.name '_phasing_MIR_der.R_cullis_anomalous'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_anomalous'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.R_cullis_centric
_item_description.description
; Residual factor R~cullis~ for centric reflections in this
derivative.
sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
R~cullis~ = ----------------------------------------
sum|Fph~obs~ - Fp~obs~|
Fp~obs~ = the observed structure factor amplitude of the native
Fph~obs~ = the observed structure factor amplitude of the
derivative
Fh~calc~ = the calculated structure factor amplitude from the
heavy atom model
sum is taken over the specified reflections
Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
& North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38.
;
_item.name '_phasing_MIR_der.R_cullis_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_Rcullis_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_der.reflns_acentric
_item_description.description
; The number of acentric reflections used in phasing for this
derivative.
;
_item.name '_phasing_MIR_der.reflns_acentric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_der.reflns_anomalous
_item_description.description
; The number of anomalous reflections used in phasing for this
derivative.
;
_item.name '_phasing_MIR_der.reflns_anomalous'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_anomalous'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_der.reflns_centric
_item_description.description
; The number of centric reflections used in phasing for this
derivative.
;
_item.name '_phasing_MIR_der.reflns_centric'
_item.category_id phasing_MIR_der
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der.ebi_reflns_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
##########################
## PHASING_MIR_DER_SITE ##
##########################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save__phasing_MIR_der_site.occupancy_anom
_item_description.description
; The relative anomalous occupancy of the atom type
present at this heavy-atom site in a given derivative.
This atom occupancy will probably be on an arbitrary scale.
;
_item.name '_phasing_MIR_der_site.occupancy_anom'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_anom_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__phasing_MIR_der_site.occupancy_anom_esd
_item_description.description
; The standard uncertainty (e.s.d.) of
_phasing_MIR_der_site.occupancy_anom.
;
_item.name '_phasing_MIR_der_site.occupancy_anom_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_anom_esd'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_default.value 0.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_anom'
_item_related.function_code associated_value
_item_type.code float
save_
save__phasing_MIR_der_site.occupancy_iso
_item_description.description
; The relative real isotropic occupancy of the atom type
present at this heavy-atom site in a given derivative.
This atom occupancy will probably be on an arbitrary scale.
;
_item.name '_phasing_MIR_der_site.occupancy_iso'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_iso_esd'
_item_related.function_code associated_esd
_item_type.code float
_item_type_conditions.code esd
save_
save__phasing_MIR_der_site.occupancy_iso_esd
_item_description.description
; The standard uncertainty (e.s.d.) of
_phasing_MIR_der_site.occupancy_iso.
;
_item.name '_phasing_MIR_der_site.occupancy_iso_esd'
_item.category_id phasing_MIR_der_site
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_der_site.ebi_occupancy_iso_esd'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_default.value 0.0
_item_related.related_name '_phasing_MIR_der_site.occupancy_iso'
_item_related.function_code associated_value
_item_type.code float
save_
#######################
## PHASING_MIR_SHELL ##
#######################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save__phasing_MIR_shell.fom_acentric
_item_description.description
; The mean value of the figure of merit m for acentric reflections
in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR_shell.fom_acentric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.fom_centric
_item_description.description
; The mean value of the figure of merit m for centric reflections
in this shell.
int P~alpha~ exp(i*alpha) dalpha
m = --------------------------------
int P~alpha~ dalpha
P~a~ = the probability that phase angle a is correct
int is taken over the range alpha = 0 to 2 pi.
;
_item.name '_phasing_MIR_shell.fom_centric'
_item.category_id phasing_MIR_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_fom_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__phasing_MIR_shell.reflns_acentric
_item_description.description
; The number of acentric reflections in this shell.
;
_item.name '_phasing_MIR_shell.reflns_acentric'
_item.category_id phasing_mir_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_acentric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_shell.reflns_anomalous
_item_description.description
; The number of anomalous reflections in this shell.
;
_item.name '_phasing_MIR_shell.reflns_anomalous'
_item.category_id phasing_mir_shell
_item.mandatory_code no
# _item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_anomalous'
# _item_aliases.dictionary ebi_extensions
# _item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__phasing_MIR_shell.reflns_centric
_item_description.description
; The number of centric reflections in this shell.
;
_item.name '_phasing_MIR_shell.reflns_centric'
_item.category_id phasing_mir_shell
_item.mandatory_code no
_item_aliases.alias_name '_phasing_MIR_shell.ebi_reflns_centric'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
############
## REFINE ##
############
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
###################################################
## Submitted by Kim Henrick ##
## Content review by Dale Tronrud - Mar 19, 1988 ##
## Editorial review by HB, JW and PMDF ##
###################################################
save__refine.correlation_coeff_Fo_to_Fc
_item_description.description
; The correlation coefficient between the observed and
calculated structure factors for reflections included in
the refinement.
The correlation coefficient is scale independent and gives
an idea of the quality of the refined model.
sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
R~corr~ = ------------------------------------------------------------
SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}
Fo = observed structure factors
Fc = calculated structure factors
<> = denotes average value of data
summation is over reflections included in the refinement
;
_item.name '_refine.correlation_coeff_Fo_to_Fc'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.correlation_coeff_Fo_to_Fc_free
_item_description.description
; The correlation coefficient between the observed and
calculated structure factors for reflections not included
in the refinement (free reflections).
The correlation coefficient is scale independent and gives
an idea of the quality of the refined model.
sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
R~corr~ = ------------------------------------------------------------
SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}
Fo = observed structure factors
Fc = calculated structure factors
<> = denotes average value of data
summation is over reflections not included (free reflections)
in the refinement
;
_item.name '_refine.correlation_coeff_Fo_to_Fc_free'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Correlation_coeff_Fo_to_Fc_free'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_ESU_B
_item_description.description
; The overall standard uncertainty (e.s.d.) of the thermal
parameters based on a maximum likelihood residual.
The overall ESU (sigma~B~)^2 gives an idea of the uncertainty
in the B values of averagely defined atoms (atoms with B values
equal to the average B value).
N_a
(sigma~B~)^2 = 8 ----------------------------------------------
sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^4}
SUM_AS = (sigma_A)^2/Sigma^2)
N_a = number of atoms
Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
E_o = normalized structure factors
sigma_{E;exp} = experimental uncertainties of normalized
structure factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = is form factor of atoms
delta_x = expected error
m = is figure of merit of phases of reflection
included in summation delta_x expected error
s = reciprocal space vector
epsilon = multiplicity of diffracting plane
summation is over all reflections included in refinement
Ref: (sigma_A estimation) "Refinement of Macromolecular
Structures by the Maximum-Likelihood Method",
Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
(ESU ML estimation) "Simplified error estimation a la
Cruickshank in macromolecular crystallography",
Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter,
no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/
;
_item.name '_refine.overall_ESU_B'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_B'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_ESU_ML
_item_description.description
; The overall standard uncertainty (e.s.d.) of the positional
parameters based on a maximum likelihood residual.
The overall ESU (sigma~X~)^2 gives an idea of the uncertainty
in the position of averagely defined atoms (atoms with
B values equal to average B value)
3 N_a
(sigma~X~)^2 = -----------------------------------------------------
8 pi^2 sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^2}
SUM_AS = (sigma_A)^2/Sigma^2)
N_a = number of atoms
Sigma = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
E_o = normalized structure factors
sigma_{E;exp} = experimental uncertainties of normalized
structure factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = is formfactor of atoms
delta_x = expected error
m = is figure of merit of phases of reflection
included in summation delta_x expected error
s = reciprocal space vector
epsilon = multiplicity of diffracting plane
summation is over all reflections included in refinement
Ref: (sigma_A estimation) "Refinement of Macromolecular
Structures by the Maximum-Likelihood Method",
Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
(ESU ML estimation) "Simplified error estimation a la
Cruickshank in macromolecular crystallography",
Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter,
no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/
;
_item.name '_refine.overall_ESU_ML'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_ML'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_ESU_R_Cruickshank_DPI
_item_description.description
; The overall standard uncertainty (e.s.d.) of the thermal
parameters based on the crystallographic R value, expressed
in a formalism known as the dispersion precisions indicator
(DPI).
The overall ESU (sigma~B~) gives an idea of the uncertainty
in the B values of averagely defined atoms (atoms with B values
equal to the average B value).
N_a
(sigma_B)^2 = 0.65 --------- (R_value)^2 (D_min)^2 C^(-2/3)
(N_o-N_p)
N_a = number of atoms
N_o = number of reflections included in refinement
N_p = number of refined parameters
R_value = conventional crystallographic R-value
D_min = maximum resolution
C = completeness of data
Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular
structures". Proc. CCP4 study weekend.
"Simplified error estimation a la Cruickshank in
macromolecular crystallography", Murshudov G. N. &
Dodson E. J. (1997). CCP4 Newsletter, no. 33.
http://www.dl.ac.uk/CCP/CCP4/newsletter33/
;
_item.name '_refine.overall_ESU_R_Cruickshank_DPI'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_R_Cruickshanks_DPI'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_ESU_R_free
_item_description.description
; The overall standard uncertainty (e.s.d.) of the thermal
parameters based on the free R value.
The overall ESU gives an idea of the uncertainty in the
B values of averagely defined atoms (atoms with B values
equal to the average B value).
N_a
(sigma_B)^2 = 0.65 ----- (R_free)^2 (D_min)^2 C^(-2/3)
N_o
N_a = number of atoms
N_o = number of reflections included in refinement
N_p = number of refined parameters
R_free = conventional free crystallographic R-value calculated
using reflections not included in refinement
D_min = maximum resolution
C = completeness of data
Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular
structures". Proc. CCP4 study weekend.
"Simplified error estimation a la Cruickshank in
macromolecular crystallography", Murshudov G. N. &
Dodson E. J. (1997). CCP4 Newsletter, no. 33.
http://www.dl.ac.uk/CCP/CCP4/newsletter33/
;
_item.name '_refine.overall_ESU_R_free'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_Overall_ESU_Rfree'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_FOM_free_R_set
_item_description.description
; Average figure of merit of phases of reflections not included
in the refinement.
This value is derived from the likelihood function.
fom = I_1(X)/I_0(X)
I_0, I_1 = zero- and first-order modified Bessel function
of the first kind
X = sigma_A |E_o| |E_c|/SIGMA
E_o, E_c = normalized observed and calculated structure
factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = formfactor of atoms
delta_x = expected error
SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
sigma_{E;exp} = uncertainties of normalized observed structure
factors
epsilon = multiplicity of diffracting plane
Ref: (sigma_A estimation) "Refinement of Macromolecular
Structures by the Maximum-Likelihood Method",
Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
;
_item.name '_refine.overall_FOM_free_R_set'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_overall_FOM_free_Rset'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
save__refine.overall_FOM_work_R_set
_item_description.description
; Average figure of merit of phases of reflections included in
the refinement.
This value is derived from the likelihood function.
fom = I_1(X)/I_0(X)
I_0, I_1 = zero- and first-order modified Bessel function
of the first kind
X = sigma_A |E_o| |E_c|/SIGMA
E_o, E_c = normalized observed and calculated structure
factors
sigma_A = <cos 2 pi s delta_x> SQRT(Sigma_P/Sigma_N)
estimated using maximum likelihood
Sigma_P = sum_{atoms in model} f^2
Sigma_N = sum_{atoms in crystal} f^2
f = is formfactor of atoms
delta_x = expected error
SIGMA = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
sigma_{E;exp} = uncertainties of normalized observed
structure factors
epsilon = multiplicity of diffracting plane
Ref: (sigma_A estimation) "Refinement of Macromolecular
Structures by the Maximum-Likelihood Method",
Murshudov, G. N., Vagin A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
;
_item.name '_refine.overall_FOM_work_R_set'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine.ebi_overall_FOM_work_Rset'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
####################
## REFINE_ANALYZE ##
####################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
###################################################
## Submitted by Kim Henrick ##
## Content review by Dale Tronrud - Jan 13, 1998 ##
## Editorial review by HB, JW and PMDF ##
###################################################
save__refine_analyze.RG_d_res_high
_item_description.description
; The value of the high-resolution cutoff in angstroms
used in calculation of the Hamilton generalized
R factor (RG) stored in refine_analyze.RG_work and
_refine_analyze.RG_free.
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
_item.name '_refine_analyze.RG_d_res_high'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_high'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.RG_d_res_low
_item_description.description
; The value of the low-resolution cutoff in angstroms
used in calculation of the Hamilton generalized
R factor (RG) stored in refine_analyze.RG_work and
_refine_analyze.RG_free.
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
_item.name '_refine_analyze.RG_d_res_low'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_d_res_low'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_analyze.RG_free
_item_description.description
; The Hamilton generalized R factor for all reflections that
satisfy the resolution limits established by
_refine_analyze.RG_d_res_high and
_refine_analyze.RG_d_res_low for the free R set of
reflections that were excluded from the refinement.
sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
Rg = Sqrt( ----------------------------------------------------------------- )
sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j
where
|Fobs| = the observed structure factor amplitudes
|Fcalc| = the calculated structure factor amplitudes
G = the scale factor which puts |Fcalc| on the
same scale as |Fobs|
w_{i,j} = the weight for the combination of the reflections
i and j.
sum_i and sum_j are taken over the specified reflections
When the covariance of the amplitude of reflection i and
reflection j is zero (i.e. the reflections are independent)
w{i,i} can be redefined as w_i and the nested sums collapsed
into one.
sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2
Rg = Sqrt( ----------------------------------- )
sum_i w_i |Fobs|_i^2
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
_item.name '_refine_analyze.RG_free'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_free'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_analyze.RG_work
_item_description.description
; The Hamilton generalized R factor for all reflections
that satisfy the resolution limits established by
_refine_analyze.RG_d_res_high and
_refine_analyze.RG_d_res_low and for those
reflections included in the working set when a free R set
of reflections are omitted from the refinement.
sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
Rg = Sqrt( ----------------------------------------------------------------- )
sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j
where
|Fobs| = the observed structure factor amplitudes
|Fcalc| = the calculated structure factor amplitudes
G = the scale factor which puts |Fcalc| on the
same scale as |Fobs|
w_{i,j} = the weight for the combination of the reflections
i and j.
sum_i and sum_j are taken over the specified reflections
When the covariance of the amplitude of reflection i and
reflection j is zero (i.e. the reflections are independent)
w{i,i} can be redefined as w_i and the nested sums collapsed
into one.
sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2
Rg = Sqrt( ----------------------------------- )
sum_i w_i |Fobs|_i^2
Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
_item.name '_refine_analyze.RG_work'
_item.category_id refine
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_work'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_analyze.RG_free_work_ratio
_item_description.description
: The observed ratio of RGfree to RGwork. The expected RG ratio
is the value that should be achievable at the end of a structure
refinement when only random uncorrelated errors exist in data
and model provided that the observations are properly weighted.
When compared with the observed RG ratio it may indicate that a
structure has not reached convergence or a model has been
over-refined with no corresponding improvement in the model.
In an unrestrained refinement the ratio of RGfree/RGwork with
only random uncorrelated errors at convergence depends only
on the number of reflections and the number of parameters as:
sqrt[(f + m) / (f - m) ]
where f = number of included structure amplitudes and
target distances, and
m = number of parameters being refined.
In the restrained case, RGfree is calculated from a random
selection of residuals including both structure amplitudes
and restraints. When restraints are included in refinement
the RG ratio requires a term for the contribution to the
minimized residual at convergence, Drest, due to those
restraints:
Drest = r - sum (w_i . (a_i)^t . (H)^-1 a_i
where
r is the number of geometrical, temperature factor and
other restraints
H is the (m,m) normal matrix given by A^t.W.A
W is the (n,n) symmetric weight matrix of the included
observations
A is the least-squares design matrix of derivatives of
order (n,m)
a_i is the ith row of A
Then the expected RGratio becomes
sqrt [ (f + (m - r + Drest))/ (f - (m - r + Drest)) ]
The expected RGfree/RGwork is not yet included in the mmCIF
dictionary.
Ref: "Rfree and the Rfree ratio. Part I: derivation of expected
values of cross-validation residuals used in macromolecular
least-squares refinement". Tickle, I. J., Laskowski, R. A.
& Moss, D.S. (1998). Acta Cryst. D, in the press.
;
_item.name '_refine_analyze.RG_free_work_ratio'
_item.category_id refine_analyze
_item.mandatory_code no
_item_aliases.alias_name '_refine_analyze.ebi_RG_work_free_ratio'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
###############################
## REFINE_FUNCT_MINIMIZED ##
###############################
#
###########################
## proposed new category ##
###########################
#
###################################################
## Submitted by Kim Henrick ##
## Content review by Dale Tronrud - Jan 13, 1998 ##
## Editorial review by HB, JW and PMDF ##
###################################################
save_REFINE_FUNCT_MINIMIZED
_category.description
; Data items in the REFINE_FUNCT_MINIMIZED category record
details about the individual terms of the function minimized
during refinement.
;
_category.id refine_funct_minimized
_category.mandatory_code no
_category_key.name '_refine_funct_minimized.type'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on RESTRAIN refinement for the CCP4 text data set
toxd.
;
;
loop_
_refine_funct_minimized.type
_refine_funct_minimized.number_terms
_refine_funct_minimized.residual
'sum(W*Delta(Amplitude)^2' 3009 1621.3
'sum(W*Delta(Plane+Rigid)^2' 85 56.68
'sum(W*Delta(Distance)^2' 1219 163.59
'sum(W*Delta(U-tempfactors)^2' 1192 69.338
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_funct_minimized.number_terms
_item_description.description
; The number of observations in this term. For example, if the
term is a residual of the X-ray data this item would contain
the number of reflections used in the refinement.
;
_item.name '_refine_funct_minimized.number_terms'
_item.category_id refine_funct_minimized
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refine_funct_minimized.NumTerms'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0
0 0
_item_type.code int
save_
save__refine_funct_minimized.residual
_item_description.description
; The residual for this term of the function which was minimized
in refinement.
;
_item.name '_refine_funct_minimized.residual'
_item.category_id refine_funct_minimized
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refine_funct_minimized.Residual'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
save_
save__refine_funct_minimized.type
_item_description.description
; The type of the function being minimized.
;
_item.name '_refine_funct_minimized.type'
_item.category_id refine_funct_minimized
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refine_funct_minimized.type'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code line
save_
save__refine_funct_minimized.weight
_item_description.description
; The weight applied to this term of the function which was
minimized in the refinement.
;
_item.name '_refine_funct_minimized.weight'
_item.category_id refine_funct_minimized
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refine_funct_minimized.weight'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item_type.code float
save_
#####################
## REFINE_LS_RESTR ##
#####################
#
###################################################
## proposed elaboration of an existing data item ##
###################################################
#
####################################################
## Submitted by Kim Henrick ##
## Content review by John Westbrook ##
## Kim Henrick approval of changes - Jan 22, 1998 ##
## Editorial review by HB, JW and PMDF ##
####################################################
save__refine_ls_restr.type
_item_description.description
; The type of the parameter being restrained.
An explicit set of data values is provided for the programs
Protin/ Prolsq (beginning with p_) and X-plor (beginning with
x_). As computer programs will evolve, these data values
are given as examples, and not as an enumeration list. Computer
programs converting a data block to a refinement table will
expect the exact form of the data values given here to be used.
;
loop_
_item.name
_item.category_id
_item.mandatory_code
'_refine_ls_restr.type' refine_ls_restr yes
'_refine_ls_restr_type.type' refine_ls_restr_type yes
loop_
_item_linked.child_name
_item_linked.parent_name
'_refine_ls_restr_type.type' '_refine_ls_restr.type'
_item_type.code line
loop_
_item_examples.case
_item_examples.detail 'p_bond_d'
'bond distance'
'p_angle_d'
'bond angle expressed as a distance'
'p_planar_d'
'planar 1,4 distance'
'p_xhbond_d'
'x-h bond distance'
'p_xhangle_d'
'x-h bond angle expressed as a distance'
'p_hydrog_d'
'hydrogen distance'
'p_special_d'
'special distance'
'p_planar'
'planes'
'p_chiral'
'chiral centers'
'p_singtor_nbd'
'single-torsion non-bonded contact'
'p_multtor_nbd'
'multiple-torsion non-bonded contact'
'p_xyhbond_nbd'
'possible (x...y) hydrogen-bond'
'p_xhyhbond_nbd'
'possible (x-h...y) hydrogen-bond'
'p_special_tor'
'special torsion angle'
'p_planar_tor'
'planar torsion angle'
'p_staggered_tor'
'staggered torsion angle'
'p_orthonormal_tor'
'orthonormal torsion angle'
'p_mcbond_it'
'main-chain bond isotropic thermal factor'
'p_mcangle_it'
'main-chain angle isotropic thermal factor'
'p_scbond_it'
'side-chain bond isotropic thermal factor'
'p_scangle_it'
'side-chain angle isotropic thermal factor'
'p_xhbond_it'
'x-h bond isotropic thermal factor'
'p_xhangle_it'
'x-h angle isotropic thermal factor'
'p_special_it'
'special isotropic thermal factor'
'RESTRAIN_Distances < 2.12'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range less than 2.12 Angtroms.
;
'RESTRAIN_Distances 2.12 < D < 2.625'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range 2.12 - 2.625 Angtroms.
;
'RESTRAIN_Distances > 2.625'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves in the distance range greater than 2.625 Angtroms.
;
'RESTRAIN_Peptide Planes'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves for peptide planes.
;
'RESTRAIN_Ring and other planes'
; For the program RESTRAIN, the root-mean-square deviation
of the difference between the values calculated from the structures
used to compile the restraints dictionary parameters and the dictionary
values themselves for rings and planes other than peptide planes.
;
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4'
.
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4'
.
save_
###########################
## REFINE_LS_RESTR_TYPE ##
###########################
#
###########################
## proposed new category ##
###########################
#
####################################################
## Submitted by Kim Henrick ##
## Content review by John Westbrook ##
## Kim Henrick approval of changes - Jan 22, 1998 ##
## Editorial review by HB, JW and PMDF ##
####################################################
save_REFINE_LS_RESTR_TYPE
_category.description
; Data items in the REFINE_LS_RESTR_TYPE category record details
about the restraints types used in the least-squares refinement.
;
_category.id refine_ls_restr_type
_category.mandatory_code no
_category_key.name '_refine_ls_restr_type.type'
loop_
_category_group.id 'inclusive_group'
'refine_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - based on RESTRAIN refinement for the CCP4 text data set
toxd.
;
;
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
'RESTRAIN_Distances < 2.12' 509 0.005 0.022
'RESTRAIN_Distances 2.12 < D < 2.625' 671 0.016 0.037
'RESTRAIN_Distances > 2.625' 39 0.034 0.043
'RESTRAIN_Peptide Planes' 59 0.002 0.010
'RESTRAIN_Ring and other planes' 26 0.014 0.010
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4' 212 0.106 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6' 288 0.101 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0' 6 0.077 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2' 10 0.114 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4' 215 0.119 .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4' 461 0.106 .
loop_
_refine_ls_restr_type.type
_refine_ls_restr_type.distance_cutoff_low
_refine_ls_restr_type.distance_cutoff_high
_refine_ls_restr_type.U_sigma_weights
'RESTRAIN_Distances < 2.12' . 2.12 .
'RESTRAIN_Distances 2.12 < D < 2.625' 2.12 2.625 .
'RESTRAIN_Distances > 2.625' 2.625 . .
'RESTRAIN_Peptide Planes' . . .
'RESTRAIN_Ring and other planes' . . .
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4' 1.2 1.4 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6' 1.4 1.6 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0' 1.8 2.0 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2' 2.0 2.2 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4' 2.2 2.4 1.800
'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4' 2.4 . 1.800
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refine_ls_restr_type.distance_cutoff_high
_item_description.description
; The upper limit in angstroms of the distance range applied to
the current restraint type.
;
_item.name '_refine_ls_restr_type.distance_cutoff_high'
_item.category_id refine_ls_restr_type
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_ls_restr_type.distance_cutoff_low
_item_description.description
; The lower limit in angstroms of the distance range applied to
the current restraint type.
;
_item.name '_refine_ls_restr_type.distance_cutoff_low'
_item.category_id refine_ls_restr_type
_item.mandatory_code no
loop_
_item_range.maximum
_item_range.minimum . 0.0
0.0 0.0
_item_type.code float
_item_units.code angstroms
save_
save__refine_ls_restr_type.type
_item_description.description
; This data item is a pointer to _refine_ls_restr.type in the
REFINE_LS_RESTR category.
;
_item.name '_refine_ls_restr_type.type'
_item.category_id refine_ls_restr_type
_item.mandatory_code yes
_item_type.code line
save_
###################
## REFLN_SYS_ABS ##
###################
#
###########################
## proposed new category ##
###########################
#
#########################################
## Submitted by Kim Henrick ##
## Content review by Paula Fitzgerald ##
## Editorial review by HB, JW and PMDF ##
#########################################
save_REFLN_SYS_ABS
_category.description
; Data items in the REFLN_SYS_ABS category record details about
the reflection data that should be systematically absent,
given the designated space group.
;
_category.id refln_sys_abs
_category.mandatory_code no
loop_
_category_key.name '_refln_sys_abs.index_h'
'_refln_sys_abs.index_k'
'_refln_sys_abs.index_l'
loop_
_category_group.id 'inclusive_group'
'refln_group'
loop_
_category_examples.detail
_category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
Example 1 - completely arbitrary
;
;
loop_
_refln_sys_abs.index_h
_refln_sys_abs.index_k
_refln_sys_abs.index_l
_refln_sys_abs.I
_refln_sys_abs.sigmaI
_refln_sys_abs.I_over_sigmaI
0 3 0 28.32 22.95 1.23
0 5 0 14.11 16.38 0.86
0 7 0 114.81 20.22 5.67
0 9 0 32.99 24.51 1.35
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
save_
save__refln_sys_abs.I
_item_description.description
; The measured value of the intensity in arbitrary units.
;
_item.name '_refln_sys_abs.I'
_item.category_id refln_sys_abs
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refln_sys_abs.I'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_related.related_name
_item_related.function_code '_refln_sys_abs.sigmaI'
associated_esd
_item_type.code float
_item_type_conditions.code esd
_item_units.code arbitrary
save_
save__refln_sys_abs.I_over_sigmaI
_item_description.description
; The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI. Used
to evaluate whether a reflection that should be systematically
absent according to the designated space group is in fact
absent.
;
_item.name '_refln_sys_abs.I_over_sigmaI'
_item.category_id refln_sys_abs
_item_aliases.alias_name '_ebi_refln_sys_abs.I_over_sigma'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
_item.mandatory_code no
_item_type.code float
save_
save__refln_sys_abs.index_h
_item_description.description
; Miller index h of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to
the cell defined by cell lengths and cell angles in the CELL
category.
;
_item.name '_refln_sys_abs.index_h'
_item.category_id refln_sys_abs
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refln_sys_abs.h'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_dependent.dependent_name
'_refln_sys_abs.index_k'
'_refln_sys_abs.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln_sys_abs.index_k
_item_description.description
; Miller index k of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to the
cell defined by cell lengths and cell angles in the CELL
category.
;
_item.name '_refln_sys_abs.index_k'
_item.category_id refln_sys_abs
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refln_sys_abs.k'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_dependent.dependent_name
'_refln_sys_abs.index_h'
'_refln_sys_abs.index_l'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln_sys_abs.index_l
_item_description.description
; Miller index l of the reflection. The values of the Miller
indices in the REFLN_SYS_ABS category must correspond to the
cell defined by cell lengths and cell angles in the CELL
category.
;
_item.name '_refln_sys_abs.index_l'
_item.category_id refln_sys_abs
_item.mandatory_code yes
_item_aliases.alias_name '_ebi_refln_sys_abs.l'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_dependent.dependent_name
'_refln_sys_abs.index_h'
'_refln_sys_abs.index_k'
_item_sub_category.id miller_index
_item_type.code int
save_
save__refln_sys_abs.sigmaI
_item_description.description
; The standard uncertainty (e.s.d.) of _refln_sys_abs.I, in
arbitrary units.
;
_item.name '_refln_sys_abs.sigmaI'
_item.category_id refln_sys_abs
_item.mandatory_code no
_item_aliases.alias_name '_ebi_refln_sys_abs.sigmaI'
_item_aliases.dictionary ebi_extensions
_item_aliases.version 1.0
loop_
_item_related.related_name
_item_related.function_code '_ebi_refln_sys_abs.I'
associated_value
_item_type.code float
_item_units.code arbitrary
save_
####
******************************************************************
John Westbrook
Rutgers, The State University of New Jersey
Department of Chemistry
610 Taylor Road
Piscataway, NJ 08854-8087
e-mail: jwest@rcsb.rutgers.edu
Ph: (732) 445-4290 Fax: (732) 445-4320
******************************************************************
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