<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""><div>Hi Joel,</div><div><br class=""></div><div> 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.</div><div><br class=""></div><div> You can circumvent the problem in your current ChimeraX using</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>marker #2 /a,b:10@CA color yellow radius 1<br class=""><br class=""></div><div>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.</div><div><br class=""></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br class=""></div><div><br class=""></div><div><blockquote type="cite" class=""><div class="">On Apr 11, 2020, at 1:12 PM, Joel Meyerson 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: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Hi,<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" 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.<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">marker #2 #1/a,b:10@CA color yellow radius 1<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">marker #2 #1/a,b:20@CA color yellow radius 1<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">marker link #2:1,2 color yellow radius 0.5<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Gives the error:<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Missing or invalid "position" argument: Expected 3 floats or object specifier<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Any suggestions on how to fix the syntax, or is there an alternative approach?<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Thanks,<o:p class=""></o:p></span></div><div style="margin: 0in 0in 0.0001pt; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Joel<o:p class=""></o:p></span></div></div><span style="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; float: none; display: inline !important;" class="">_______________________________________________</span><br style="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; 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