<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Unfortunately that option doesn’t offer control over the exact amount of inter-block spacing, just whether there is some or none. To change the size of the inter-block spacing, you would need to edit the Python code. Namely <your Chimera>/share/MultAlignViewer/SeqCanvas.py, line 1271. That line should be:<div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>self.blockGap = 15</div><div class=""><br class=""></div><div class="">You would change 15 to whatever value you prefer. I believe the value is in pixels.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div></div>P.S. If you are on a Mac, then “<your Chimera>” is Chimera.app/Contents/Resources.<br class="Apple-interchange-newline"><br class="Apple-interchange-newline">
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<br class=""><div><blockquote type="cite" class=""><div class="">On Feb 9, 2017, at 9:29 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Jackie,<br class="">Yes, see the sequence window menu: "Preferences… Appearance. " There are several options for spacing, font, and coloring, including “Space between wrapped blocks.”<br class=""><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavprefs" class="">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavprefs</a>><br class=""><br class="">Best,<br class="">Elaine<br class=""><br class=""><blockquote type="cite" class="">On Feb 9, 2017, at 12:45 AM, Jacqueline Vitali <<a href="mailto:jackie.vitali@gmail.com" class="">jackie.vitali@gmail.com</a>> wrote:<br class=""><br class="">Elaine,<br class=""><br class="">Thank you so much. Doing it by hand is the easiest. <br class="">Also, is there a way to increase the distance between wrapped blocks? <br class=""><br class="">Jackie Vitali<br class="">Cleveland State University<br class=""><br class="">On Wed, Feb 8, 2017 at 1:39 PM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class="">You can also:<br class=""><br class="">(1) hide/show the header lines (Conservation, Consensus, etc.) using the sequence window Headers menu<br class="">(2) change how Conservation is calculated (sequence window Preferences… Headers)<br class="">(3) add your own headers with quantities or symbols, e.g. put stars over the columns with superfamily-conserved residues<br class=""><br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers" class="">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#headers</a>><br class=""><br class="">Elaine<br class=""><br class=""><blockquote type="cite" class="">On Feb 8, 2017, at 8:30 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu" class="">meng@cgl.ucsf.edu</a>> wrote:<br class=""><br class="">Hi Jackie,<br class="">You can draw boxes (we call them “regions”) in the alignment wherever you want with click and drag, and then change their colors using the Region Browser.<br class=""><br class="">Multalign Viewer:<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html" class="">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/framemav.html</a>><br class=""><br class="">Regions, including how to create them manually:<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#regions" class="">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#regions</a>><br class=""><br class="">Region Browser (click the square color wells to change colors):<br class=""><<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#regionbrowser" class="">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#regionbrowser</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class=""><br class=""><br class=""><blockquote type="cite" class="">On Feb 7, 2017, at 10:57 PM, Jacqueline Vitali <<a href="mailto:jackie.vitali@gmail.com" class="">jackie.vitali@gmail.com</a>> wrote:<br class=""><br class="">Elaine,<br class=""><br class="">I would appreciate it very much if you could let me know how to highlight specific conserved residues in a sequence alignment between 2 proteins with chimera using the MAV? I highlight helices and beta sheets with colors, conservation between the 2 proteins is shown with the blocks on top. But there are 15-20 residues conserved in the superfamily of proteins and i would like to use blocks around them or highlight them in different color. In other words, 60 residues are conserved between the 2 proteins and 20 are special and need to be shown in a different way.<br class=""><br class="">I hope my question is clear.<br class=""><br class="">Thank you in advance.<br class=""><br class="">Jackie Vitali<br class="">Cleveland State University<br class=""></blockquote></blockquote><br class=""><br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""><br class=""></div></div></blockquote></div><br class=""></div></body></html>