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<p class="MsoNormal">Hi Tom,<o:p></o:p></p>
<p class="MsoNormal">Thanks for the info and the hack. I just tested it out I can display both markers. However, strangely enough the second marker seems not to appear as an entry in the model panel and when I try to create the marker link using the command
in my previous email I get this error:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">marker link command requires exactly 2 markers, got 1<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks also for introducing a change in the daily release. I’ll be sure to test it.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Joel<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">Tom Goddard <goddard@sonic.net><br>
<b>Date: </b>Saturday, April 11, 2020 at 4:41 PM<br>
<b>To: </b>Joel Meyerson <jrm2008@med.cornell.edu><br>
<b>Cc: </b>"chimerax-users@cgl.ucsf.edu" <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>[EXTERNAL] Re: [chimerax-users] syntax on marker and marker link placement<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Joel,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> ChimeraX has trouble when a command has two model or atom specifiers next to each other in a command. It considers them as a single argument, ignoring the space between them. So we try to make our commands not take two adjacent specifier
arguments. So to fix this I just changed the marker command so you have to say "marker #2 position #1/A,B:10@CA" with the position keyword added. This will be in tonight's builds. The "marker segment" command also requires the "position" keyword now.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> You can circumvent the problem in your current ChimeraX using<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">marker #2 /a,b:10@CA color yellow radius 1<o:p></o:p></p>
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<p class="MsoNormal">dropping the #1 from the atom specifier assuming you have no other structure with chains A,B open. Surprisingly this works because the marker set specifier is only expecting a model so it doesn't merge the chain specifiers that follow.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Tom<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Apr 11, 2020, at 1:12 PM, Joel Meyerson wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi,<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">I have a question about marker and marker link syntax. Suppose model #1 has chains A and B, and that chains A and B form a homodimer where each subunit has the same residue numbering. I would like to place a marker at the midpoint between
alpha-carbons of position 10 on A and 10 on B. In turn, I'd like another marker at the midpoint between position 20 on each of the two subunits. I would then like to draw a linker between the two markers. I would expect the following syntax to work, but I
get an error.<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">marker #2 #1/a,b:10@CA color yellow radius 1<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">marker #2 #1/a,b:20@CA color yellow radius 1<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">marker link #2:1,2 color yellow radius 0.5<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Gives the error:<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Missing or invalid "position" argument: Expected 3 floats or object specifier<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Any suggestions on how to fix the syntax, or is there an alternative approach?<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Thanks,<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Joel<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
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