only foldseek has "showTable" option for making results open but not …

…shown

docs/user/commands/foldseek.html

@@ -98,7 +98,8 @@ <h3 class="usage"><a href="usageconventions.html">Usage</a>:
 which facilitates exploring large sets of protein structures 
 by efficiently showing them in 3D as backbone traces and in
 2D as sequence alignment schematics or scatter plots based on conformation.
-Even if the table is not shown, the results can still be analyzed in those
+Even with <b>showTable false</b>, however, 
+the results can still be analyzed in those
 ways by referring to them by name (<b>fs1</b> or <b>fs2</b>) in
 <a href="similarstructures.html"><b>similarstructures</b></a> commands.
 The <a href="../tools/log.html"><b>Log</b></a> reports the name
@@ -163,5 +164,5 @@ <h3 class="usage"><a href="usageconventions.html">Usage</a>:
 
 <hr>
 <address>UCSF Resource for Biocomputing, Visualization, and Informatics / 
-October 2024</address>
+November 2024</address>
 </body></html>

docs/user/commands/similarstructures.html

@@ -252,7 +252,10 @@ <h3>Similar Structures Analysis</h3>
 <a href="../tools/log.html"><b>Log</b></a> when a search is run,
 and the names of open sets can be listed in the 
 <a href="../tools/log.html"><b>Log</b></a> with
-<a href="#list"><b>similarstructures list</b></a>.
+<a href="#list"><b>similarstructures list</b></a>. However,
+the only way to get a set of results that is open but not shown in the table
+is to use the <b>showTable false</b> option of the search command
+<a href="foldseek.html"><b>foldseek</b></a>.
 </p><p>
 <a name="hit-ID"></a>
 The <i>hit-ID</i> for a structure from the 

docs/user/tools/foldseek.html

@@ -241,11 +241,14 @@ <h3>Similar Structures List</h3>
 Doing another search or opening a file of previously saved results replaces the
 contents of the <b>Similar Structures</b> table, since (currently) the tool 
 only allows showing one set of results at a time.
-However, the sets of results are assigned names such as 
-fs1, fs2, mm1, mm2, bl1, and bl2 that can be used in analysis commands 
-<!-- is this only true when you used showTable false?? -->
-even if the corresponding results are not shown.
-These names are reported in the <a href="log.html"><b>Log</b></a>.
+Sets of results are assigned names such as fs1, fs2, mm1, mm2, bl1, and bl2 
+that can be used in analysis commands even if the corresponding results 
+are not shown. However, the only way to get a set of results that is open
+but not shown in the table is to use the <b>showTable false</b> option of 
+the search command <a href="../commands/foldseek.html"><b>foldseek</b></a>.
+The names of currently open sets can be listed with the command 
+<a href="../commands/similarstructures.html#list"><b>similarstructures 
+list</b></a>.
 </p>
 
 <a name="options"></a>
@@ -567,6 +570,7 @@ <h3>Cluster Plot</h3>
 &ndash; scroll the table of results to the corresponding row 
 <li><b>Show reference atoms</b>
 &ndash; display the reference &alpha;-carbons as spheres
+and <a href="../selection.html">select</a> them
 <li><b>Select reference atoms</b>
 &ndash; <a href="../selection.html">select</a> the reference &alpha;-carbons
 </ul>
@@ -619,6 +623,8 @@ <h3>Ligands</h3>
 PDB ID and chain ID of its source structure (<i>e.g.</i>, <b>2cml_B</b>).
 Pausing the cursor over a residue in the graphics window shows
 its name and chain ID in a pop-up balloon.
+</p><p>
+See also: <a href="https://alphafill.eu/" target="_blank">AlphaFill</a>
 </p>
 
 <a name="notes"></a>
@@ -657,5 +663,5 @@ <h3>References</h3>
 
 <hr>
 <address>UCSF Resource for Biocomputing, Visualization, and Informatics /
-October 2024</address>
+November 2024</address>
 </body></html>