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<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Hi Eric,<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>This sounds great. I use aliases which are not commands also of
course. That’s why I suggested a setable flag as an option in the alias
command to indicate that “this” alias is a command and should go to
the menu. As I haven’t needed ‘^’ yet, using it as you
suggest would work for me.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Here is an example for highlighting a particular protein mutant
(we have many mutants we use for mapping. Some give positive results, some don’t).<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>General for all positive mutants:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>alias pos_map_HSS color white $1; represent
stick $1; setattr m stickScale 3 $1; color blue $1@n=; color red $1@o=; color
green $1@s=; ribcol c_HSS $1;<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Specific mutant:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>alias HSS_987N #0:987.B<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Highlight the mutant:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>pos_map_HSS HSS_987N<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>New alias for new menu:<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'>alias ^pos_HSS_987N pos_map_HSS HSS_987N<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>There can also be a paired alias to turn off the highlighting. Now
I can do all on or all off by typing, but having the menu with all the
individual mutants listed would be highly desirable.<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Tim<o:p></o:p></span></p>
<p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;
font-family:"Courier New"'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
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<div style='border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm'>
<p class=MsoNormal><b><span style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span
style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> Eric Pettersen
[mailto:pett@cgl.ucsf.edu] <br>
<b>Sent:</b> Wednesday, 04 February 2009 20:06<br>
<b>To:</b> Richmond Timothy J.<br>
<b>Cc:</b> chimera-dev@cgl.ucsf.edu; chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [chimera-dev] alias menu<o:p></o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal>On Feb 4, 2009, at 5:09 AM, Richmond Timothy J. wrote:<o:p></o:p></p>
</div>
<p class=MsoNormal><br>
<br>
<o:p></o:p></p>
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<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Dear Chimera Developers,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
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<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Perhaps I have missed it, but I would find a menu for selected
aliases very useful. Having returned to Chimera from PyMol recently, it would
be great to have an option for the alias command that allowed the particular
alias to be listed in a separate window and ran the alias by clicking on the
alias name listed there.<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Best regards,<o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'> <o:p></o:p></span></p>
</div>
<div>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:black'>Tim<o:p></o:p></span></p>
</div>
</div>
</div>
<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal>Hi Tim,<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><span class=apple-tab-span> </span>As
Elaine pointed out in her reply, aliases are frequently used as shorthands for
long atom specs rather than as replacements for complete commands.
However, the form of the alias command that uses '^' (so that matching
only occurs at the start of the line) typically <i>is</i> used to define full
command aliases. <o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
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<div>
<p class=MsoNormal><span class=apple-tab-span> </span>So
my thinking is this: aliases defined with the '^' character would be placed in
an 'Aliases' top-level menu (created on the fly as needed). Such aliases
would automatically be remembered across Chimera invocations (and populate an
Aliases menu). The menu could be torn-off (except on Aqua) to make a
stand-alone window. Those aliases could be deleted as normal with the
~alias command (which would remove them from the menu and no longer remember
then in subsequent Chimeras).<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal><span class=apple-tab-span> </span>Would
this be good enough?<o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><o:p> </o:p></p>
</div>
<div>
<p class=MsoNormal>--Eric<o:p></o:p></p>
</div>
<p class=MsoNormal><o:p> </o:p></p>
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<p style='margin:0cm;margin-bottom:.0001pt'><span class=apple-converted-space><span
style='font-size:9.5pt;font-family:"Helvetica","sans-serif";color:black'>
</span></span><span style='font-size:9.5pt;font-family:"Helvetica","sans-serif";
color:black'>Eric Pettersen<o:p></o:p></span></p>
<p style='margin:0cm;margin-bottom:.0001pt'><span class=apple-converted-space><span
style='font-size:9.5pt;font-family:"Helvetica","sans-serif";color:black'>
</span></span><span style='font-size:9.5pt;font-family:"Helvetica","sans-serif";
color:black'>UCSF Computer Graphics Lab<o:p></o:p></span></p>
<p style='margin:0cm;margin-bottom:.0001pt'><span class=apple-converted-space><span
style='font-size:9.5pt;font-family:"Helvetica","sans-serif";color:black'>
</span></span><span style='font-size:9.5pt;font-family:"Helvetica","sans-serif";
color:black'><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:9.5pt;font-family:"Helvetica","sans-serif";
color:black'><o:p> </o:p></span></p>
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<p class=MsoNormal><o:p> </o:p></p>
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