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fix MolProbity spelling
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aozalevsky committed Mar 28, 2024
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12 changes: 6 additions & 6 deletions templates/full_validation_pdf.html
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Expand Up @@ -143,7 +143,7 @@ <h2 align="center">{{ date }}</h2>
<li><em><a href='https://github.com/ihmwg/python-ihm'>Python-IHM</a> Version {{ python_ihm_version }}</em></li>

{% if molprobity_version is not none %}
<li><em><a href='http://molprobity.biochem.duke.edu/'>Molprobity</a> Version {{ molprobity_version }}</em></li>
<li><em><a href='http://molprobity.biochem.duke.edu/'>MolProbity</a> Version {{ molprobity_version }}</em></li>
{% endif %}

{% if sas|length > 0 and sasdb_sascif|length > 0 %}
Expand Down Expand Up @@ -222,12 +222,12 @@ <h3 align="center">
<em>This validation report contains model quality assessments for all structures, data quality assessment for SAS datasets and fit to model assessments for SAS datasets. Data quality and fit to model assessments for other datasets and model uncertainty are under development. Number of plots is limited to {{MAXPLOTS}}.</em>
</p>

<!-- Molprobity or excluded volume -->
<!-- MolProbity or excluded volume -->
<div class="box text-center container-fluid no-padding" align='center' style="break-inside: avoid;">
{% if disclaimer == 0 %}
{% if assess_excluded_volume == 'Not applicable' %}
<h5 align=center>
Model Quality: Molprobity Analysis
Model Quality: MolProbity Analysis
</h5>
{% else %}
<h5 align=center>
Expand All @@ -242,7 +242,7 @@ <h5 align=center>
{% endfor %}
{% elif disclaimer == 1 %}
<p align="justify">
<em>Molprobity assessments and/or excluded volume assessments can not be evaluated for this current model.</em>
<em>MolProbity assessments and/or excluded volume assessments can not be evaluated for this current model.</em>
</p>
{% endif %}
</div>
Expand Down Expand Up @@ -594,7 +594,7 @@ <h5 align= left>Excluded volume satisfaction <a class='help1' style='background-
{{ write_table(excluded_volume) }}

{% else %}
<!-- Molprobity -->
<!-- MolProbity -->

<!-- Bond outliers -->
<h5 align=center>
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{% endif %}
{% endif %}

<!-- End Molprobity -->
<!-- End MolProbity -->
{% endif %}

<!-- End Model Quality -->
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4 changes: 2 additions & 2 deletions templates/main.html
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Expand Up @@ -98,7 +98,7 @@ <h3 align="center">

{% if disclaimer %}
<p align="justify">
<em>Molprobity assessments and/or excluded volume assessments can not be evaluated for this current model.
<em>MolProbity assessments and/or excluded volume assessments can not be evaluated for this current model.
</em>
</p>
{% endif %}
Expand Down Expand Up @@ -190,7 +190,7 @@ <h3></h3>
<li><em><a href='https://github.com/ihmwg/python-ihm'>Python-IHM</a> Version {{ python_ihm_version }}</em></li>

{% if molprobity_version is not none %}
<li><em><a href='http://molprobity.biochem.duke.edu/'>Molprobity</a> Version {{ molprobity_version }}</em></li>
<li><em><a href='http://molprobity.biochem.duke.edu/'>MolProbity</a> Version {{ molprobity_version }}</em></li>
{% endif %}

{% if sas|length > 0 and sasdb_sascif|length > 0 %}
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2 changes: 1 addition & 1 deletion templates/references.csv
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Expand Up @@ -55,7 +55,7 @@ scikit-learn | https://jmlr.csail.mit.edu/papers/v12/pedregosa11a.html | Pedrego
trRosetta | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6983395/ | Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, Baker D. Improved protein structure prediction using predicted interresidue orientations. Proc Natl Acad Sci U S A. 2020;117(3):1496-1503.
trRossetta | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6983395/ | Yang J, Anishchenko I, Park H, Peng Z, Ovchinnikov S, Baker D. Improved protein structure prediction using predicted interresidue orientations. Proc Natl Acad Sci U S A. 2020;117(3):1496-1503.
PROSESS | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896095/ | Berjanskii M, Liang Y, Zhou J, et al. PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res. 2010;38(Web Server issue):W633-W640.
Molprobity | https://pubmed.ncbi.nlm.nih.gov/29067766/ | Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2018 Jan;27(1):293-315.
MolProbity | https://pubmed.ncbi.nlm.nih.gov/29067766/ | Williams CJ, Headd JJ, Moriarty NW, Prisant MG, Videau LL, Deis LN, Verma V, Keedy DA, Hintze BJ, Chen VB, Jain S, Lewis SM, Arendall WB 3rd, Snoeyink J, Adams PD, Lovell SC, Richardson JS, Richardson DC. MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2018 Jan;27(1):293-315.
multicoil2 | https://pubmed.ncbi.nlm.nih.gov/21901122/ | Trigg J, Gutwin K, Keating AE, Berger B. Multicoil2: predicting coiled coils and their oligomerization states from sequence in the twilight zone. PLoS One. 2011;6(8).
mCSM | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904523/ | Pires DE, Ascher DB, Blundell TL. mCSM: predicting the effects of mutations in proteins using graph-based signatures. Bioinformatics. 2014;30(3):335-342.
QRNAS | http://genesilico.pl/software/stand-alone/qrnas | Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM. QRNAS: software tool for refinement of nucleic acid structures. BMC Struct Biol. 2019;19(1):5.
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6 changes: 3 additions & 3 deletions templates/validation_help.html
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Expand Up @@ -42,7 +42,7 @@
<li><a href="#modelquality" style="color: #003366;">5. Model Quality Assessment</a>
<ul>
<li><a href="#exv" style="color: #003366;">5.1a Excluded Volume Analysis</a></li>
<li><a href="#molprobity" style="color: #003366;">5.1b Molprobity Analysis </a></li>
<li><a href="#molprobity" style="color: #003366;">5.1b MolProbity Analysis </a></li>
</ul>
</li>

Expand Down Expand Up @@ -83,7 +83,7 @@

<p class=ex2 align='justify'><a name='understanding'><i>1.2. Data quality assessment :</i></a> Data quality assessments are only available for Small Angle Scattering datasets (SAS). This section was developed in collaboration with the SASBDB community. For details on the metrics, guidelines, and recommendations used, refer the 2017 community article <a href='https://pubmed.ncbi.nlm.nih.gov/28876235/'>(Trewhella et al. 2017)</a>. All experimental datasets used to build the model are listed, however, validation criteria for other experimental datasets are currently under development.</p>

<p class=ex2 align='justify'><a name='understanding'><i>1.3. Model quality assessment :</i></a> Model quality for models at atomic resolution is assessed using Molprobity <a href='https://pubmed.ncbi.nlm.nih.gov/29067766/'> (Williams et al. 2018)</a>, consistent with <a href='https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#model_quality'>PDB</a>. Model quality for coarse-grained or multi-resolution structures are assessed by computing excluded volume satisfaction based on reported distances and sizes of beads in the structures.</p>
<p class=ex2 align='justify'><a name='understanding'><i>1.3. Model quality assessment :</i></a> Model quality for models at atomic resolution is assessed using MolProbity <a href='https://pubmed.ncbi.nlm.nih.gov/29067766/'> (Williams et al. 2018)</a>, consistent with <a href='https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#model_quality'>PDB</a>. Model quality for coarse-grained or multi-resolution structures are assessed by computing excluded volume satisfaction based on reported distances and sizes of beads in the structures.</p>

<p class=ex2 align='justify'><a name='understanding'><i> 1.4. Fit to data used to build the model :</i></a> Fit to data used to build the model is only available for SAS datasets. This section was developed in collaboration with the SASBDB <a href='https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383894/'>(Valentini et al. 2015)</a>. For details on the metrics, guidelines, and recommendations used, refer the 2017 community article <a href='https://pubmed.ncbi.nlm.nih.gov/28876235/'>(Trewhella et al. 2017)</a>. All experimental datasets used to build the model are listed, however, validation criteria for other experimental datasets are currently under development.</p>

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<p class=ex2 align='center' ><b><u> <a name='modelquality'>5. Model Quality Assessment </a></u> </b></p>
<p class=ex2 align='justify' > Excluded volume assessments are performed for coarse-grained structures and MolProbity analysis is performed for atomic structures.</p>
<p class=ex2 align='justify' ><a name='exv'><i>5.1a. Excluded Volume Analysis :</i></a> Excluded volume violation is defined as percentage of overlaps between coarse-grained beads in a structure. This percentage is obtained by dividing the number of overlaps/violations by the total number of pair distances in a structure. An overlap or violation between two beads occurs if the distance between the two beads is less than the sum of their radii <a href='https://pubmed.ncbi.nlm.nih.gov/29539637/'>(S. J. Kim et al. 2018)</a>. </p>
<p class=ex2 align='justify' ><a name='molprobity'> <i>5.1b. Molprobity Analysis :</i></a> Molprobity analysis for atomic structures reported is consistent with PDB standards for X-ray structures <a href='https://pubmed.ncbi.nlm.nih.gov/29067766/'>(Williams et al. 2018)</a>. Summarized information is available in both the HTML and PDF reports. Detailed information is available for download as csv files, both from the HTML and the PDF reports. Please refer to the <a href='https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#model_quality'>PDB user guide</a> for details. </p>
<p class=ex2 align='justify' ><a name='molprobity'> <i>5.1b. MolProbity Analysis :</i></a> MolProbity analysis for atomic structures reported is consistent with PDB standards for X-ray structures <a href='https://pubmed.ncbi.nlm.nih.gov/29067766/'>(Williams et al. 2018)</a>. Summarized information is available in both the HTML and PDF reports. Detailed information is available for download as csv files, both from the HTML and the PDF reports. Please refer to the <a href='https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#model_quality'>PDB user guide</a> for details. </p>
<p style=margin-bottom:0.5cm;> </p>
</div>
</div>
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