<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">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.<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 11, 2020, at 1:56 PM, Joel Meyerson <<a href="mailto:jrm2008@med.cornell.edu" class="">jrm2008@med.cornell.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Tom,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">marker link command requires exactly 2 markers, got 1<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks also for introducing a change in the dailyo release. I’ll be sure to test it.<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Best,<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Joel<o:p class=""></o:p></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="border-style: solid none none; border-top-width: 1pt; border-top-color: rgb(181, 196, 223); padding: 3pt 0in 0in;" class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><b class=""><span style="font-size: 12pt;" class="">From:<span class="Apple-converted-space"> </span></span></b><span style="font-size: 12pt;" class="">Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class=""><b class="">Date:<span class="Apple-converted-space"> </span></b>Saturday, April 11, 2020 at 4:41 PM<br class=""><b class="">To:<span class="Apple-converted-space"> </span></b>Joel Meyerson <<a href="mailto:jrm2008@med.cornell.edu" class="">jrm2008@med.cornell.edu</a>><br class=""><b class="">Cc:<span class="Apple-converted-space"> </span></b>"<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>" <<a href="mailto:chimerax-users@cgl.ucsf.edu" class="">chimerax-users@cgl.ucsf.edu</a>><br class=""><b class="">Subject:<span class="Apple-converted-space"> </span></b>[EXTERNAL] Re: [chimerax-users] syntax on marker and marker link placement<o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi Joel,<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> 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 class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> You can circumvent the problem in your current ChimeraX using<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><p class="MsoNormal" style="margin: 0in 0in 12pt; font-size: 11pt; font-family: Calibri, sans-serif;">marker #2 /a,b:10@CA color yellow radius 1<o:p class=""></o:p></p></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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 class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Tom<o:p class=""></o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div></div><div class=""><blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">On Apr 11, 2020, at 1:12 PM, Joel Meyerson wrote:<o:p class=""></o:p></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div class=""><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi,<span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">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: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">marker #2 #1/a,b:10@CA color yellow radius 1<span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">marker #2 #1/a,b:20@CA color yellow radius 1<span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">marker link #2:1,2 color yellow radius 0.5<span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Gives the error:<span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Missing or invalid "position" argument: Expected 3 floats or object specifier<span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Any suggestions on how to fix the syntax, or is there an alternative approach?<span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""> <span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks,<span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div class=""><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Joel<span style="font-size: 12pt;" class=""><o:p class=""></o:p></span></div></div><div style="margin: 0in 0in 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">_______________________________________________<br class="">ChimeraX-users mailing list<br class=""></span><a href="mailto:ChimeraX-users@cgl.ucsf.edu" style="color: blue; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">ChimeraX-users@cgl.ucsf.edu</span></a><span style="font-size: 9pt; font-family: Helvetica;" class=""><br class="">Manage subscription:<br class=""></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=" style="color: blue; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica;" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</span></a></div></div></blockquote></div></div></div></blockquote></div><br class=""></div></body></html>