<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:0 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal">Hi Tom,<o:p></o:p></p>
<p class="MsoNormal">I used a simple workaround by creating the markers separately based on alpha-carbon position, getting each of their x,y,z coordinates, creating a new pair of markers using the coordinates, and then drawing the line between the new markers.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal">Joel<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<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 5:25 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>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">Ok. The hack I suggested of "marker #2 /a,b:10@CA" in fact does not work and confuses the marker command into making a new model #2 each time you run it even though model #2 already exists, because no markerset #2/A exists. It should
have given an error about this. You'll need to get get tomorrow's fixed marker command and use the "position" keyword.
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Tom<o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On Apr 11, 2020, at 1:56 PM, Joel Meyerson <<a href="mailto:jrm2008@med.cornell.edu">jrm2008@med.cornell.edu</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Hi Tom,<o:p></o:p></p>
</div>
<div>
<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>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">marker link command requires exactly 2 markers, got 1<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Thanks also for introducing a change in the dailyo release. I’ll be sure to test it.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Best,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Joel<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<div>
<p class="MsoNormal"><b><span style="font-size:12.0pt">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt">Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Saturday, April 11, 2020 at 4:41 PM<br>
<b>To:<span class="apple-converted-space"> </span></b>Joel Meyerson <<a href="mailto:jrm2008@med.cornell.edu">jrm2008@med.cornell.edu</a>><br>
<b>Cc:<span class="apple-converted-space"> </span></b>"<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>" <<a href="mailto:chimerax-users@cgl.ucsf.edu">chimerax-users@cgl.ucsf.edu</a>><br>
<b>Subject:<span class="apple-converted-space"> </span></b>[EXTERNAL] Re: [chimerax-users] syntax on marker and marker link placement</span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal">Hi Joel,<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<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>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> You can circumvent the problem in your current ChimeraX using<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt">marker #2 /a,b:10@CA color yellow radius 1<o:p></o:p></p>
</div>
<div>
<div>
<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>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Tom<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal">On Apr 11, 2020, at 1:12 PM, Joel Meyerson wrote:<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<div>
<div>
<p class="MsoNormal">Hi,<o:p></o:p></p>
</div>
</div>
<div>
<div>
<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.<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">marker #2 #1/a,b:10@CA color yellow radius 1<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">marker #2 #1/a,b:20@CA color yellow radius 1<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">marker link #2:1,2 color yellow radius 0.5<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Gives the error:<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Missing or invalid "position" argument: Expected 3 floats or object specifier<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Any suggestions on how to fix the syntax, or is there an alternative approach?<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class="MsoNormal">Joel<o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
ChimeraX-users mailing list<br>
</span><a href="mailto:ChimeraX-users@cgl.ucsf.edu"><span style="font-size:9.0pt;font-family:Helvetica">ChimeraX-users@cgl.ucsf.edu</span></a><span style="font-size:9.0pt;font-family:Helvetica"><br>
Manage subscription:<br>
</span><a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFAg&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=JnYzuUa3E5p4u7qrfPzeZV8LIgMpwauz4WIvX7NJIi8&m=fzZblJRz4mXN2MmDMiN5zccNMmjMAHuZXC-PM7zbX-Q&s=EnyBgOSNOVHTtyTXzIch74ammVljsIkLkmF1uSqvIP8&e="><span style="font-size:9.0pt;font-family:Helvetica">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a><o:p></o:p></p>
</div>
</div>
</blockquote>
</div>
</div>
</blockquote>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
</div>
</body>
</html>