fix typos and links

aozalevsky · Mar 28, 2024 · a6a6b19 · a6a6b19
1 parent c9bd499
commit a6a6b19
Showing 1 changed file with 8 additions and 8 deletions.
diff --git a/templates/validation_help.html b/templates/validation_help.html
@@ -65,7 +65,7 @@ <h5 style="color: #003366;">
               <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>
             <li>
@@ -109,15 +109,15 @@ <h5 style="color: #003366;">
           </p> 
 
           <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.
+            <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 to 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.
+            <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.
+            <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 to 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>
@@ -147,7 +147,7 @@ <h5 style="color: #003366;">
           <ul style="list-style-type:none;">
             <li>
               <p class=ex2>
-                <i><a name='overview'>2.1.1. Model quality:</a></i> For atomic structures, MolProbity is used for evaluation. We evaluate bond outliers, side chain outliers, clash score, rotamer satisfaction, and ramachandran dihedral satisfaction <a href='https://pubmed.ncbi.nlm.nih.gov/29067766/'>(Williams et al. 2018)</a> . Details on MolProbity evaluation and tables can be found <a href='https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#model_quality'>here</a>. For coarse-grained structures of beads, we evaluate excluded volume satisfaction. An excluded volume violation or overlap 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>. Excluded volume satisfaction is the percentage of pair distances in a structure that are not violated (higher values are better).
+                <i><a name='overview'>2.1.1. Model quality:</a></i> For atomic structures, MolProbity is used for evaluation. We evaluate bond outliers, side chain outliers, clash score, rotamer satisfaction, and Ramachandran dihedral satisfaction <a href='https://pubmed.ncbi.nlm.nih.gov/29067766/'>(Williams et al. 2018)</a> . Details on MolProbity evaluation and tables can be found <a href='https://www.wwpdb.org/validation/2017/XrayValidationReportHelp#model_quality'>here</a>. For coarse-grained structures of beads, we evaluate excluded volume satisfaction. An excluded volume violation or overlap 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>. Excluded volume satisfaction is the percentage of pair distances in a structure that are not violated (higher values are better).
               </p>
             </li>
             <li>
@@ -209,7 +209,7 @@ <h5 style="color: #003366;">
           </p>
 
           <p class=ex2 align='justify'>
-            <a name='pofr'><i>4.4. SAS: P(r) Analysis:</i></a> P(r) represents the distribution of distances between all pairs of atoms within the particle weighted by the respective electron densities <a href='https://onlinelibrary.wiley.com/doi/abs/10.1107/S002188988001179X'> (Moore 1980) </a>. 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. The value of P(r) should be zero beyond r=D<sub>max</sub>.
+            <a name='pofr'><i>4.4. SAS: P(r) Analysis:</i></a> P(r) represents the distribution of distances between all pairs of atoms within the particle weighted by the respective electron densities <a href='https://onlinelibrary.wiley.com/doi/abs/10.1107/S002188988001179X'> (Moore 1980) </a>. 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. The value of P(r) should be zero beyond r=D<sub>max</sub>.
           </p>
 
           <p class=ex2 align='justify'>
@@ -239,7 +239,7 @@ <h5 style="color: #003366;">
           </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.
+            <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>
@@ -304,7 +304,7 @@ <h5 style="color: #003366;">
           </figure>
 
           <p class=ex2 align='justify'>
-            <a name='goodness'><i>6.1. SAS:  &#x3A7;&#178; Goodness of Fit Assessment:</i></a> Model and fits displayed below were obtained from SASBDB. χ² values are a measure of fit of the model to data. A perfect fit has a χ² value of zero. (<a href='https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5586245/#bb95'>Trewhella et al. 2013</a>,<a href='https://pubmed.ncbi.nlm.nih.gov/22800408/'>Schneidman-Duhovny, Kim, and Sali 2012</a>, and <a href='https://pubmed.ncbi.nlm.nih.gov/23495971/'> Rambo and Tainer 2013</a>).
+            <a name='goodness'><i>6.1. SAS:  &#x3A7;&#178; Goodness of Fit Assessment:</i></a> Model fits displayed in this section are obtained from SASBDB. χ² values are a measure of fit of the model to data. A perfect fit has a χ² value of 1.0. (<a href='https://pubmed.ncbi.nlm.nih.gov/23747111/'>Trewhella et al. 2013</a>, <a href='https://pubmed.ncbi.nlm.nih.gov/22800408/'>Schneidman-Duhovny, Kim, and Sali 2012</a>, and <a href='https://pubmed.ncbi.nlm.nih.gov/23495971/'>Rambo and Tainer 2013</a>).
           </p>
 
           <p class=ex2 align='justify'>