From 5a2874d51c89108948540b8693dd6003272c3ebd Mon Sep 17 00:00:00 2001 From: ubuntu Date: Wed, 21 Feb 2024 10:57:46 -0800 Subject: [PATCH] updated links to relative to the server --- templates/data_quality.html | 12 ++++++------ templates/formodeling.html | 4 ++-- templates/layout.html | 16 +++++++++------- templates/main.html | 8 ++++---- templates/model_composition.html | 12 ++++++------ templates/model_quality.html | 14 +++++++------- 6 files changed, 34 insertions(+), 32 deletions(-) diff --git a/templates/data_quality.html b/templates/data_quality.html index b25e1db6..b91c4dc2 100644 --- a/templates/data_quality.html +++ b/templates/data_quality.html @@ -9,7 +9,7 @@
-

Data quality? +

Data quality?

@@ -43,7 +43,7 @@
- SAS:Scattering profile? + SAS:Scattering profile?

SAS data used in this integrative model was obtained from {{sasdb_code_html|length|int}} deposited SASBDB entry (entries). @@ -76,7 +76,7 @@

- Key experimental estimates? + Key experimental estimates?

Molecular weight (MW) estimates from experiments and analysis: true molecular weight can be compared to the Porod estimate from scattering profiles. @@ -99,7 +99,7 @@

{% if sas|length > 0 and sasdb_sascif|length > 0 %}
- Flexibility analysis ? + Flexibility analysis ?
{% endif %}
@@ -127,7 +127,7 @@
- Pair-distance distribution analysis? + Pair-distance distribution analysis?

P(r) analysis: P(r) represents the distribution of distances between all pairs of atoms within the particle weighted by the respective electron densities. P(r) is the Fourier transform of I(s) (and vice versa). Rg can be estimated from integrating the P(r) function. Agreement between the P(r) and Guinier-determined Rg (table below) is a good measure of the self-consistency of the SAS profile. Rg is a measure for the overall size of a macromolecule; e.g. a protein with a smaller Rg is more compact than a protein with a larger Rg, provided both have the same molecular weight (MW). The point where P(r) is decaying to zero is called Dmax and represents the maximum size of the particle. @@ -156,7 +156,7 @@

-
Guinier analysis ? +
Guinier analysis ?

Guinier analysis: agreement between the P(r) and Guinier-determined Rg (table below) is a good measure of the self-consistency of the SAS profile. Molecular weight estimates can also be compared to Porod and sample molecular weights for consistency. diff --git a/templates/formodeling.html b/templates/formodeling.html index 726c9873..cae4a985 100644 --- a/templates/formodeling.html +++ b/templates/formodeling.html @@ -10,7 +10,7 @@

- Fit of model to data used for modeling? + Fit of model to data used for modeling?

@@ -35,7 +35,7 @@
Fit of model(s) to SAS data
- Cormap p-value analysis of fits ? + Cormap p-value analysis of fits ?
{% if number_of_fits > 0 %}

diff --git a/templates/layout.html b/templates/layout.html index c8b3f2c4..53d46b35 100644 --- a/templates/layout.html +++ b/templates/layout.html @@ -5,13 +5,15 @@ {%- block title -%}PDB-Dev Validation Report{%- endblock -%} - {% if html_mode == 'local' %} + {% else %} - - + + + + {% endif %} @@ -41,7 +43,7 @@ {% if html_mode == 'local' %} PDBDEV.org {% else %} - PDBDEV.org + PDBDEV.org {% endif %}

PDB-Dev

@@ -83,7 +85,7 @@
  • - About
    Validation     + About
    Validation
  • @@ -227,7 +229,7 @@
  • - Validation
    Help     + Validation
    Help
    • @@ -245,7 +247,7 @@
    {% if html_mode == 'local' %} wwpdb {% else %} - wwpdb + wwpdb {% endif %}
    diff --git a/templates/main.html b/templates/main.html index 44bf2fc6..0f631fd6 100644 --- a/templates/main.html +++ b/templates/main.html @@ -7,7 +7,7 @@

    - + {{ID_R[0]}}

    @@ -26,7 +26,7 @@
    Download Summary Table
    - Model + Model
    @@ -78,7 +78,7 @@
    Download Summary Table

    Overall quality - ? + ?

    This validation report contains model quality assessments for all structures. For more detail for each assessment, use the dropdown menus at the top of this page. @@ -174,7 +174,7 @@

    Acknowledgements

    • -

      Development of integrative model validation metrics, implementation of a model validation pipeline, and creation of a validation report for integrative structures, are funded by NSF ABI awards (DBI-1756248, DBI-2112966, DBI-2112967, DBI-2112968, and DBI-1756250). The PDB-Dev team and members of Sali lab contributed model validation metrics and software packages.

      +

      Development of integrative model validation metrics, implementation of a model validation pipeline, and creation of a validation report for integrative structures, are funded by NSF ABI awards (DBI-1756248, DBI-2112966, DBI-2112967, DBI-2112968, and DBI-1756250). The PDB-Dev team and members of Sali lab contributed model validation metrics and software packages.

    • Implementation of validation methods for SAS data and SAS-based models are funded by RCSB PDB (grant number DBI-1832184). Dr. Stephen Burley, Dr. John Westbrook, and Dr. Jasmine Young from RCSB PDB, Dr. Jill Trewhella, Dr. Helen M. Berman, Dr. Dina Schneidman, and members of SASBDB repository are acknowledged for their advice and support in implementing SAS validation methods.

      diff --git a/templates/model_composition.html b/templates/model_composition.html index afe2a278..c74a8de5 100644 --- a/templates/model_composition.html +++ b/templates/model_composition.html @@ -11,7 +11,7 @@

      - Ensemble information? + Ensemble information?

      {% if num_ensembles < 2 %}

      This entry consists of {{num_ensembles|int}} distinct ensemble.

      @@ -29,7 +29,7 @@

      - Summary? + Summary?

      @@ -45,7 +45,7 @@

      -

      Entry composition? +

      Entry composition?

      {% if number_of_molecules < 2 %} There is {{number_of_molecules|int}} unique type of model in this entry. @@ -70,7 +70,7 @@

      Entry composition
      -

      Datasets used for modeling ?

      +

      Datasets used for modeling ?

      {% if number_of_datasets < 2 %} There is {{number_of_datasets|int}} unique dataset used to build the models in this entry. {% else %} @@ -88,7 +88,7 @@

      Datasets used for modeling
      -

      Representation ?

      +

      Representation ?

      This entry has only one representation and includes {{Rigid_Body|int}} rigid bodies and {{Flexible_Unit|int}} flexible units.

      {{ write_table(RB_list) }} @@ -103,7 +103,7 @@

      Representation

      - Methodology and software? + Methodology and software?

      {% if Protocols_number < 2 %} diff --git a/templates/model_quality.html b/templates/model_quality.html index 4dd7028a..b45411dd 100644 --- a/templates/model_quality.html +++ b/templates/model_quality.html @@ -8,7 +8,7 @@
      -

      Model quality?

      +

      Model quality?

      For models with atomic structures, molprobity analysis is performed. For models with coarse-grained or multi-scale structures, excluded volume analysis is performed.

      {% if disclaimer > 0 %} @@ -18,7 +18,7 @@

      Model quality? +

      Excluded volume satisfaction?
      Excluded volume satisfaction for the models in the entry are listed below.

      @@ -27,7 +27,7 @@
      Excluded volume satisfactionStandard geometry: bond outliers? + Standard geometry: bond outliers?

      {% if molp_b|length > 1 %} @@ -42,7 +42,7 @@
      {% endif %}
      - Standard geometry: angle outliers? + Standard geometry: angle outliers?

      {% if molp_a|length > 1 %} @@ -58,7 +58,7 @@
      {% if clashscore_list|length > 1 %}
      - Too-close contacts? + Too-close contacts?

      The following all-atom clashscore is based on a MolProbity analysis. All-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The table below contains clashscores for all the models in this entry. @@ -79,7 +79,7 @@

      {% if ramascore|length > 1 %}
      - Torsion angles: Protein backbone? + Torsion angles: Protein backbone?

      In the following table, Ramachandran outliers are listed. The Analysed column shows the number of residues for which the backbone conformation was analysed. @@ -98,7 +98,7 @@

      {% if rotascore|length > 1 %}
      - Torsion angles : Protein sidechains? + Torsion angles : Protein sidechains?
      In the following table, sidechain rotameric outliers are listed. The Analysed column shows the number of residues for which the sidechain conformation was analysed.