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updated links to relative to the server
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ubuntu committed Feb 21, 2024
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12 changes: 6 additions & 6 deletions templates/data_quality.html
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<div class="card-header" style="background-color: #FFF;">
<div class="row">
<div class="col-lg-12">
<h4 class="ex2" align="center"><u><a name='first'>Data quality</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#dataquality'>?</a>
<h4 class="ex2" align="center"><u><a name='first'>Data quality</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='/validation_help.html#dataquality'>?</a>
</h4>
</div>
</div>
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<div class="col-lg-12">
<!-- potential nesting inconsistency -->
<h5 class= ex2 align= center>
<u><a name=firstI>SAS:Scattering profile</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#scattering'>?</a>
<u><a name=firstI>SAS:Scattering profile</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='/validation_help.html#scattering'>?</a>
</h5>
<p align=justify>
SAS data used in this integrative model was obtained from {{sasdb_code_html|length|int}} deposited SASBDB entry (entries).
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<div class="col-lg-12">
<div class="card-header" style="background-color: #FFF;">
<h5 class= ex2 align= center>
<u><a name=firstE>Key experimental estimates</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#expt'>?</a>
<u><a name=firstE>Key experimental estimates</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='/validation_help.html#expt'>?</a>
</h5>
<p class=ex2 align='justify'>
<u>Molecular weight (MW) estimates from experiments and analysis</u>: true molecular weight can be compared to the Porod estimate from scattering profiles.
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<div class="col-lg-12">
{% if sas|length > 0 and sasdb_sascif|length > 0 %}
<h5 class= ex2 align= center>
<u><a name=firstF>Flexibility analysis</a> </u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#flexibility'>?</a>
<u><a name=firstF>Flexibility analysis</a> </u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='/validation_help.html#flexibility'>?</a>
</h5>
{% endif %}
</div>
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<!-- header -->
<div class="col-lg-12">
<h5 align= center>
<u><a name=firstP>Pair-distance distribution analysis</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#pofr'>?</a>
<u><a name=firstP>Pair-distance distribution analysis</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='/validation_help.html#pofr'>?</a>
</h5>
<p class=ex2 align='justify'>
<u>P(r) analysis:</u> 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). R<sub>g</sub> can be estimated from integrating the P(r) function. Agreement between the P(r) and Guinier-determined R<sub>g</sub> (table below) is a good measure of the self-consistency of the SAS profile. R<sub>g</sub> is a measure for the overall size of a macromolecule; e.g. a protein with a smaller R<sub>g</sub> is more compact than a protein with a larger R<sub>g</sub>, provided both have the same molecular weight (MW). The point where P(r) is decaying to zero is called D<sub>max</sub> and represents the maximum size of the particle.
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<div class="row">
<!-- description -->
<div class="col-lg-12">
<h5 class= ex2 align= center><u><a name=firstG> Guinier analysis </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#guinier'>?</a>
<h5 class= ex2 align= center><u><a name=firstG> Guinier analysis </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='/validation_help.html#guinier'>?</a>
</h5>
<p class=ex2 align='justify'>
<u> Guinier analysis:</u> agreement between the P(r) and Guinier-determined R<sub>g</sub> (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.
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4 changes: 2 additions & 2 deletions templates/formodeling.html
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<div class="row">
<div class="col-lg-12">
<h4 class="ex2" align="center">
<u><a name='first'>Fit of model to data used for modeling</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#fittodata'>?</a>
<u><a name='first'>Fit of model to data used for modeling</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='/validation_help.html#fittodata'>?</a>
</h4>
</div>
</div>
Expand All @@ -35,7 +35,7 @@ <h5 class= ex2 align= center><u> Fit of model(s) to SAS data</u></h5>
<div class="row">
<div class="col-lg-6">
<h5 class= ex2 align= center>
<u><a name='second'>Cormap p-value analysis of fits </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='https://pdb-dev.wwpdb.org/validation_help.html#cormap'>?</a>
<u><a name='second'>Cormap p-value analysis of fits </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href='/validation_help.html#cormap'>?</a>
</h5>
{% if number_of_fits > 0 %}
<p class =ex2>
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16 changes: 9 additions & 7 deletions templates/layout.html
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<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<title>{%- block title -%}PDB-Dev Validation Report{%- endblock -%}</title>
<!-- add bootstrap css file -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css">
{% if html_mode == 'local' %}
<link rel="stylesheet" href="static/css/main.css">
<link rel="stylesheet" href="static/css/layout.css">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css">
{% else %}
<link rel="stylesheet" href="https://pdb-dev.wwpdb.org/css/main.css">
<link rel="stylesheet" href="https://pdb-dev.wwpdb.org/css/layout.css">
<link rel="stylesheet" href="/css/bootstrap.min.css">
<link rel="stylesheet" href="/css/main.css">
<link rel="stylesheet" href="/css/layout.css">
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.5.2/css/bootstrap.min.css">
{% endif %}

<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js"></script>
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{% if html_mode == 'local' %}
<img src="static/images/logon.png" class="float-left" alt="PDBDEV.org" height="100" width="110" style="margin-top: 0px; margin-bottom: 0px" />
{% else %}
<img src="https://pdb-dev.wwpdb.org/images/logon.png" class="float-left" alt="PDBDEV.org" height="100" width="110" style="margin-top: 0px; margin-bottom: 0px" />
<img src="/images/logon.png" class="float-left" alt="PDBDEV.org" height="100" width="110" style="margin-top: 0px; margin-bottom: 0px" />
{% endif %}
<p>
<h1 style="margin-left: 0px; color: #003366;">PDB-Dev</h1>
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<!-- About validation -->
<li class="nav-item mr-4 dropdown">
<a class="btn btn-primary " href="https://pdb-dev.wwpdb.org/about_validation.html"><span class="overview">About <br> Validation</span></a>
<a class="btn btn-primary " href="/about_validation.html"><span class="overview">About <br> Validation</span></a>
</li>
<li class="nav-item mr-4 dropdown">
<a class="dropdown-toggle" data-toggle="dropdown"><button type="button" class="btn btn-primary" onclick=window.location='main.html';>Validation <br> Overview</button></a>
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</div>
</li>
<li class="nav-item mr-4 dropdown">
<a class="btn btn-primary " href="https://pdb-dev.wwpdb.org/validation_help.html"><span class="overview">Validation <br> Help</span></a>
<a class="btn btn-primary " href="/validation_help.html"><span class="overview">Validation <br> Help</span></a>
</li>
</ul>
</div>
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{% if html_mode == 'local' %}
<img src="static/images/wwpdb-logo11.png" alt="wwpdb" height="35px" width="160px"></a>
{% else %}
<img src="https://pdb-dev.wwpdb.org/images/wwpdb-logo11.png" alt="wwpdb" height="35px" width="160px"></a>
<img src="/images/wwpdb-logo11.png" alt="wwpdb" height="35px" width="160px"></a>
{% endif %}
</div>
<div class="col-sm-6">
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8 changes: 4 additions & 4 deletions templates/main.html
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<div class="col-lg-4">
<div class="card-header" style="background-color: #FFFFFF; border-color:#003366; height: 29rem;">
<h3 align=center>
<a href=https://pdb-dev.wwpdb.org/entry.html?{{ID_R[0]}}>
<a href=/entry.html?{{ID_R[0]}}>
{{ID_R[0]}}
</a>
</h3>
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</a>
</div>
<div class="box text-center container-fluid no-padding">
<img src=https://pdb-dev.wwpdb.org/images/{{ID_R[0]}}_resize_1.png class=image-fluid alt=Model Image style=width:300px align=center>
<img src=/images/{{ID_R[0]}}_resize_1.png class=image-fluid alt=Model Image style=width:300px align=center>
</div>
</div>
<!-- end card header -->
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<div class="card-header" style="background-color: #FFFFFF; border-color:#003366;">
<h3 align="center">
<a name='qual'>Overall quality</a>
<a class='help' title='help' style="background-color:#228B22;color:#000000;text-decoration:none font-size=16px" href="https://pdb-dev.wwpdb.org/validation_help.html#overview">?</a>
<a class='help' title='help' style="background-color:#228B22;color:#000000;text-decoration:none font-size=16px" href="/validation_help.html#overview">?</a>
</h3>
<p align="justify">
<em>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.
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<p align="justify"> <em>Acknowledgements</em> </p>
<ul style="list-style-type:none;">
<li>
<p align="justify"><em>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 <a href='https://pdb-dev.wwpdb.org/about.html'>PDB-Dev team</a> and members of <a href='https://www.salilab.org/'>Sali lab </a>contributed model validation metrics and software packages. </em></p>
<p align="justify"><em>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 <a href='/about.html'>PDB-Dev team</a> and members of <a href='https://www.salilab.org/'>Sali lab </a>contributed model validation metrics and software packages. </em></p>
</li>
<li>
<p align="justify"><em>Implementation of validation methods for SAS data and SAS-based models are funded by <a href='https://www.rcsb.org/'>RCSB PDB </a> (grant number DBI-1832184). Dr. Stephen Burley, Dr. John Westbrook, and Dr. Jasmine Young from <a href='https://www.rcsb.org/'>RCSB PDB</a>, Dr. Jill Trewhella, Dr. Helen M. Berman, Dr. Dina Schneidman, and members of <a href='https://www.sasbdb.org/'>SASBDB </a> repository are acknowledged for their advice and support in implementing SAS validation methods. </em></p>
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12 changes: 6 additions & 6 deletions templates/model_composition.html
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<div class="col-lg-12">
<div class="card-header" style="background-color: #FFF;">
<h4 align='center'>
<u><a name='ensemble'>Ensemble information</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="https://pdb-dev.wwpdb.org/validation_help.html#ensemble">?</a>
<u><a name='ensemble'>Ensemble information</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="/validation_help.html#ensemble">?</a>
</h4>
{% if num_ensembles < 2 %}
<p class ="ex2"><i>This entry consists of {{num_ensembles|int}} distinct ensemble.</i></p>
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<div class="col-lg-12">
<div class="card-header" style="background-color: #FFF;">
<h4 class="ex2" align="center">
<u><a name=summary>Summary</a></u><a class="help" title="help" style="background-color:#228B22;color:#000000;text-decoration:none font-size=16px" href="https://pdb-dev.wwpdb.org/validation_help.html#summary">?</a>
<u><a name=summary>Summary</a></u><a class="help" title="help" style="background-color:#228B22;color:#000000;text-decoration:none font-size=16px" href="/validation_help.html#summary">?</a>
</h4>

<p align="justify">
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<div class="row">
<div class="col-lg-12">
<div class="card-header" style="background-color: #FFF;">
<h4 class="ex2" align="center"><u><a name='entry'>Entry composition</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="https://pdb-dev.wwpdb.org/validation_help.html#entry">?</a>
<h4 class="ex2" align="center"><u><a name='entry'>Entry composition</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="/validation_help.html#entry">?</a>
</h4>
{% if number_of_molecules < 2 %}
<i>There is {{number_of_molecules|int}} unique type of model in this entry.</i>
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<div class="row">
<div class="col-lg-12">
<div class="card-header" style="background-color: #FFF;">
<h4 class="ex2" align="center"><u><a name='data'>Datasets used for modeling </a></u> <a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="https://pdb-dev.wwpdb.org/validation_help.html#datasets">?</a></h4>
<h4 class="ex2" align="center"><u><a name='data'>Datasets used for modeling </a></u> <a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="/validation_help.html#datasets">?</a></h4>
{% if number_of_datasets < 2 %}
<i>There is {{number_of_datasets|int}} unique dataset used to build the models in this entry.</i>
{% else %}
Expand All @@ -88,7 +88,7 @@ <h4 class="ex2" align="center"><u><a name='data'>Datasets used for modeling </a>
<div class="row">
<div class="col-lg-12">
<div class="card-header" style="background-color: #FFF;">
<h4 class="ex2" align="center"><u><a name="representation">Representation </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="https://pdb-dev.wwpdb.org/validation_help.html#representation">?</a> </h4>
<h4 class="ex2" align="center"><u><a name="representation">Representation </a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="/validation_help.html#representation">?</a> </h4>
<p class="ex2" align="justify"><i>This entry has only one representation and includes {{Rigid_Body|int}} rigid bodies and {{Flexible_Unit|int}} flexible units.</i></p>

{{ write_table(RB_list) }}
Expand All @@ -103,7 +103,7 @@ <h4 class="ex2" align="center"><u><a name="representation">Representation </a></
<div class="col-lg-12">
<div class="card-header" style="background-color: #FFF;">
<h4 class="ex2" align="center">
<u><a name="methods">Methodology and software</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="https://pdb-dev.wwpdb.org/validation_help.html#software">?</a>
<u><a name="methods">Methodology and software</a></u><a class='help' title='help' style='background-color:#228B22;color:#000000;text-decoration:none font-size=16px' href="/validation_help.html#software">?</a>
</h4>
<!-- Protocols summary -->
{% if Protocols_number < 2 %}
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