fix pymol mistakex

docs/pymol.html

@@ -438,7 +438,7 @@ <h2 data-number="2.2" class="anchored" data-anchor-id="choose-representation-and
 <h2 data-number="2.3" class="anchored" data-anchor-id="create-new-object-andor-get-rid-of-what-you-dont-want"><span class="header-section-number">2.3</span> 3. Create new object and/or get rid of what you don’t want</h2>
 <p>If we want to work only with some objects or chains in the PDB file, you can do it in several ways. There are several options but you need to <strong>show the sequence</strong> (Menu Display or button <strong>S</strong> on the <u>botton-right corner</u>).</p>
 <p>You can remove objects (Option 1A or 1B) or copy a selection to a new object (Option 2A or 2B). You can test all with the instructions below, but I find more convenient to use command line alternatives (1B and 2B).</p>
-<p><em>Note: The options below are alternative ways to get the same results. Try only one option each time starting over from 6KI3 structure.</em></p>
+<p><em>⚠️️ Note that the options 1 and 2 below are alternative ways to get the same results. Try only one option each time starting over from 6KI3 structure.⚠️❗️</em></p>
 <ul>
 <li><p>Option 1A: select in the sequence panel the sequence you want to remove and remove it</p>
 <div class="sourceCode" id="cb9"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a>remove sele</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div></li>

docs/search.json

@@ -766,7 +766,7 @@
     "href": "pymol.html#create-new-object-andor-get-rid-of-what-you-dont-want",
     "title": "Pymol Practice",
     "section": "2.3 3. Create new object and/or get rid of what you don’t want",
-    "text": "2.3 3. Create new object and/or get rid of what you don’t want\nIf we want to work only with some objects or chains in the PDB file, you can do it in several ways. There are several options but you need to show the sequence (Menu Display or button S on the botton-right corner).\nYou can remove objects (Option 1A or 1B) or copy a selection to a new object (Option 2A or 2B). You can test all with the instructions below, but I find more convenient to use command line alternatives (1B and 2B).\nNote: The options below are alternative ways to get the same results. Try only one option each time starting over from 6KI3 structure.\n\nOption 1A: select in the sequence panel the sequence you want to remove and remove it\nremove sele\nOption 1B: use command line\n\nStep 1: First you need to see the composition of your structure\n\nget_chains 6KI3\nselect chain A\nselect chain B\n#to see who is who\n\nStep 2: select the chains you want to remove and remove them\n\nselect kk, chain A or chain C or chain D or chain E\ndelete kk\nOption 2A: Select in the sequence panel the sequence or whole chains you want to keep: A > “Copy to object” or “extract to object” will allow to work independently with that portion without removing the rest. Just click on the object to disable.\nOption 2B: use command line\n\nStep 1: Select and create:\n\nselect kk, chain B or chain F or chain G or chain H\ncreate monomer, kk\n\nOr directly create an object with your selected chains:\ncreate monomer, chain B or chain F or chain G or chain H\n\nStep 2: Now you can remove the original object (if you wish)\nremove 6KI3\n\n\nSome interesting points about selection on Pymol:\n\nUnnamed selection are temporarily named “sele” and replaced after every select command execution.\nSelections can be renamed in the A (action menu on the left) or by command line : https://pymolwiki.org/index.php/Set_name\nMultiple selection can be also done but syntax is tricky: https://pymolwiki.org/index.php/Selection_Algebra\n\n\nCreate your own representation of the monomer ternary complex (protein + metal cofactor + DNA)"
+    "text": "2.3 3. Create new object and/or get rid of what you don’t want\nIf we want to work only with some objects or chains in the PDB file, you can do it in several ways. There are several options but you need to show the sequence (Menu Display or button S on the botton-right corner).\nYou can remove objects (Option 1A or 1B) or copy a selection to a new object (Option 2A or 2B). You can test all with the instructions below, but I find more convenient to use command line alternatives (1B and 2B).\n⚠️️ Note that the options 1 and 2 below are alternative ways to get the same results. Try only one option each time starting over from 6KI3 structure.⚠️❗️\n\nOption 1A: select in the sequence panel the sequence you want to remove and remove it\nremove sele\nOption 1B: use command line\n\nStep 1: First you need to see the composition of your structure\n\nget_chains 6KI3\nselect chain A\nselect chain B\n#to see who is who\n\nStep 2: select the chains you want to remove and remove them\n\nselect kk, chain A or chain C or chain D or chain E\ndelete kk\nOption 2A: Select in the sequence panel the sequence or whole chains you want to keep: A > “Copy to object” or “extract to object” will allow to work independently with that portion without removing the rest. Just click on the object to disable.\nOption 2B: use command line\n\nStep 1: Select and create:\n\nselect kk, chain B or chain F or chain G or chain H\ncreate monomer, kk\n\nOr directly create an object with your selected chains:\ncreate monomer, chain B or chain F or chain G or chain H\n\nStep 2: Now you can remove the original object (if you wish)\nremove 6KI3\n\n\nSome interesting points about selection on Pymol:\n\nUnnamed selection are temporarily named “sele” and replaced after every select command execution.\nSelections can be renamed in the A (action menu on the left) or by command line : https://pymolwiki.org/index.php/Set_name\nMultiple selection can be also done but syntax is tricky: https://pymolwiki.org/index.php/Selection_Algebra\n\n\nCreate your own representation of the monomer ternary complex (protein + metal cofactor + DNA)"
   },
   {
     "objectID": "pymol.html#bonus-track-more-info-and-useful-resources-about-pymol.",

pymol.qmd

@@ -246,8 +246,8 @@ You can remove objects (Option 1A or 1B) or copy a selection to a new object
 (Option 2A or 2B). You can test all with the instructions below, but I find more
 convenient to use command line alternatives (1B and 2B).
 
-*Note: The options below are alternative ways to get the same results. Try only
-one option each time starting over from 6KI3 structure.*
+*⚠️️ Note that the options 1 and 2 below are alternative ways to get the same results. Try only
+one option each time starting over from 6KI3 structure.⚠️❗️*
 
 -   Option 1A: select in the sequence panel the sequence you want to remove and
     remove it