<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi all,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I have made my intended improvements to the single-sequence viewer now and the new version is in the daily build (which you can get by going to <a href="http://www.cgl.ucsf.edu/chimera">www.cgl.ucsf.edu/chimera</a> and following the "Daily Builds" link). I encourage people who use the sequence viewer a lot to fetch the new version and let me know what you like and what you don't.</div><div><br></div><div>--Eric</div><div><br><div apple-content-edited="true"> <span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 16px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>Eric Pettersen</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> <span class="Apple-converted-space"> </span></span>UCSF Computer Graphics Lab</font></p><p style="margin: 0.0px 0.0px 0.0px 0.0px"><font face="Helvetica" size="5" style="font: 16.0px Helvetica"><span class="Apple-converted-space"> </span><a href="http://www.cgl.ucsf.edu">http://www.cgl.ucsf.edu</a></font></p><br class="Apple-interchange-newline"></div></span> </div><br><div><div>On Dec 18, 2008, at 10:20 AM, Eric Pettersen wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Christos,<br><span class="Apple-tab-span" style="white-space:pre"> </span>In previous releases, there were two tools that showed sequences: <br>the sequence viewer (single sequences) and Multalign Viewer (sequence <br>alignments). We plan to show additional information with sequences <br>(e.g. UniProt markups) and as a step in that direction we decided to <br>unify our presentation of sequence info by making MAV capable of <br>showing single sequences. That way, the work to show sequence <br>information in the user interface won't have to be duplicated each <br>time we add something.<br><span class="Apple-tab-span" style="white-space:pre"> </span>So, rather than restore the old sequence viewer, what I would prefer <br>to do is make the MAV interface better for showing single sequences. <br>Would it help if single sequences were combined in a single dialog, <br>like in the previous sequence viewer? I don't think that's too hard <br>to do. As for color, I think you're right that for a single sequence <br>it makes more sense to show that columns as black, since there is no <br>conservation per se down the column. I can easily change that. You <br>can too, in fact, by choosing Preferences->Analysis in the MAV window <br>and changing "Residue letter coloring" to "black" (the preference will <br>be carried over to future MAV dialogs).<br><span class="Apple-tab-span" style="white-space:pre"> </span>So what other changes would make the MAV version of the sequence <br>version more usable? I guess this is actually a general question to <br>everybody...<br><br>--Eric<br><br>On Dec 17, 2008, at 5:05 PM, Gatsogiannis, Christos wrote:<br><br><blockquote type="cite">Hi all,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">i ve just installed the latest daily build version and iīve noticed <br></blockquote><blockquote type="cite">that the sequence viewer has a new "look".<br></blockquote><blockquote type="cite">However, i have difficulties to get used to it...<br></blockquote><blockquote type="cite">Some examples:<br></blockquote><blockquote type="cite">-when i want to view the sequence of a pdb file containing seven <br></blockquote><blockquote type="cite">chains, i get seven different pop-up windows (...) showing the <br></blockquote><blockquote type="cite">sequences corresponding to the seven different chain IDīs....<br></blockquote><blockquote type="cite">-Moreover, it isnīt so "easy" anymore to select aminoacids directly <br></blockquote><blockquote type="cite">in the sequence viewer (e.g. too many colors) and therefore now iīm <br></blockquote><blockquote type="cite">selecting residues using only the command line..<br></blockquote><blockquote type="cite">My colleagues also prefer the older version..<br></blockquote><blockquote type="cite">is there a simple way to install the latest chimera version but keep <br></blockquote><blockquote type="cite">the old version of the sequence viewer?<br></blockquote><blockquote type="cite">Thanks!<br></blockquote><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users<br></div></blockquote></div><br></div></body></html>