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<p style="margin-top:0;margin-bottom:0">Greetings,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">thank you for your quick reply about the "non-bug" request relating to the initial display and the explanation. After your reply I searched more intensely in the documentation and indeed found page <span><span style="font-family: Consolas, Courier, monospace;">help:user/autostyle.html</span>
with these details about the number of chains.</span></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">As I am preparing to demonstrate ChimeraX in the department (tutorial I find that some inherent aspect of the Automatic Styling (Smart Initial Display) is very quickly lost.
<i>e.g.</i> simply by clicking on the "Show atoms" button in the <span>Molecular display toolbar and then the "Hide atoms".</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span>I found commands for selection at <a href="http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html" class="OWAAutoLink" id="LPlnk792149" previewremoved="true">http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html</a> which
are useful and one can reconstruct the initial display. </span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span>As I example I am using myoglobin (<span style="font-family: Consolas, Courier, monospace;">1mbo.</span>) </span><span style="font-size: 12pt;">The molecule opens as a ribbon, heteroatoms as stick models, the iron
ion as sphere, and AA close to the ligands as sticks as well.</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
Simply pressing the "Show atoms" button will display all water molecules as small spheres.</span></p>
<p style="margin-top:0;margin-bottom:0"><span>But now if I click "Hide atoms" only the ribbon is left.</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span>Yesterday I tried to find a way to select
<i>heteroatoms</i> in general and use the </span><span style="white-space: pre-wrap; font-size: 12pt;"><span style="font-family: Consolas, Courier, monospace;">sel ~ sel</span> selection inversion found on the
<a href="http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html" class="OWAAutoLink" id="LPlnk239157" previewremoved="true">
pipermail</a> but that was not the best solution.</span></p>
<p style="margin-top:0;margin-bottom:0"><span style="white-space: pre-wrap; font-size: 12pt;"><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span style="white-space: pre-wrap; font-size: 12pt;"><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">Today
I could</span><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;"> reconstruct the initial display with these
commands if all I did was to toggle the "Show atoms" and "Hide atoms" buttons:</span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-family: Consolas, Courier, monospace;">show ions</span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-family: Consolas, Courier, monospace;">show ligand</span></p>
<p style="margin-top:0;margin-bottom:0"><span><span style="font-family: Consolas, Courier, monospace;">select ligand:<3.8 & protein</span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span><span style="font-family: Consolas, Courier, monospace;">show selAtoms</span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">For novices this is a bit complicated to understand.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Therefore I <span style="font-size: 12pt;">would like to suggest the addition of a "<span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">A</span><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">utomatic
S</span><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">tyling (Smart Initial Display)</span>" button,
perhaps at the First position in the <span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">Molecular display
toolbar. </span></span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;"><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;"><br>
</span></span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;"><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">I
firmly believe that this would avoid lots of frustration for many new users!</span></span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;"><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;"><br>
</span></span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;"><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;">P.S.
One more thing: would it be possible to Copy from the built-in browser to Paste elsewhere as I am trying to do with the email address? </span></span></p>
<p style="margin-top:0;margin-bottom:0"><span style="font-size: 12pt;"><span style="font-family: Calibri, Helvetica, sans-serif, Helvetica, EmojiFont, "Apple Color Emoji", "Segoe UI Emoji", NotoColorEmoji, "Segoe UI Symbol", "Android Emoji", EmojiSymbols; font-size: 16px;"><br>
</span></span></p>
<p style="margin-top:0;margin-bottom:0">Sincerely,</p>
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<p></p>
<p style="font-family:Calibri,Arial,Helvetica,sans-serif,"Apple Color Emoji","Segoe UI Emoji",NotoColorEmoji,"Segoe UI Symbol","Android Emoji",EmojiSymbols; font-size:16px">
<span style="font-family:Garamond,Georgia,serif">Jean-Yves Sgro</span></p>
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