<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Sabuj,<DIV> Multalign Viewer should be able to read either SCF format. Let me know if it doesn't.</DIV><DIV> You can hack your Chimera distribution to get the behavior you asked for originally without too much effort. The Multalign Viewer source is in <your installation>/share/MultAlignViewer. You will need to change the files Consensus.py and SeqCanvas.py. In Consensus, change the value of capitalizeAt from 0.8 to 1.1 (never produce capital letters). In the evaluate() method, move:</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV> if num == len(self.seqs):</DIV><DIV> self.conserved[pos] = 1</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>out of the surrounding 'if' (which is now never true). In SeqCanvas, in the layout() method there is a colorConsensus() embedded function. Remove the test for uppercase characters and reverse the logic so that it returns 'red' for unconserved and 'black' otherwise.</DIV><DIV> I should offer better control over consensus properties, especially now that I am working on supporting phylogenetic trees and will be showing consensus/conservation lines for subtrees. Another related thing I'm working on is supporting Python plugins that add header lines that not only depict characters (in various colors) but simple shapes such as rectangles, circles, arrows, etc.</DIV><DIV><BR><DIV> <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>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>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="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</A></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><BR><DIV><DIV>On Jul 29, 2005, at 10:58 AM, Sabuj Pattanayek wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks for mentioning the SCF file. I can create a script to create the file from the alignment. Does the SCF parser in the multialign viewer read the new format or the old format (I guess newer)?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sabuj Pattanayek</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Elaine Meng wrote:</DIV> <BR><BLOCKQUOTE type="cite"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi all,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I have a clustal aln file or a fasta file with two nearly identical<SPAN class="Apple-converted-space"> </SPAN>aligned protein sequences. When I view them in the multialign<SPAN class="Apple-converted-space"> </SPAN>viewer I would like to change the color of the consensus style.<SPAN class="Apple-converted-space"> </SPAN>That is, residues which are both identical should be just black<SPAN class="Apple-converted-space"> </SPAN>(rather than red and capitalized) and residues that are not<SPAN class="Apple-converted-space"> </SPAN>identical should be red (or some other color that contrasts against<SPAN class="Apple-converted-space"> </SPAN>black). Is there anyway to do this?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Better yet would it be possible to not use the consensus at all and<SPAN class="Apple-converted-space"> </SPAN>color the entire non-matching column a color of my choice?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Sabuj Pattanayek</DIV> <BR></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi Sabuj,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Currently there is no way to change the Consensus line contents from<SPAN class="Apple-converted-space"> </SPAN>the user interface. All you can do is to turn it off entirely (from<SPAN class="Apple-converted-space"> </SPAN>the Multalign Viewer window, Preferences... Analysis and set the<SPAN class="Apple-converted-space"> </SPAN>"Consensus style" to "none").<SPAN class="Apple-converted-space"> </SPAN>If your alignment just has two<SPAN class="Apple-converted-space"> </SPAN>sequences, however, all the columns where there is no bar in the<SPAN class="Apple-converted-space"> </SPAN>Conservation histogram when the "Conservation style" is set to<SPAN class="Apple-converted-space"> </SPAN>"identity histogram," or no asterisk when the "Conservation style" is<SPAN class="Apple-converted-space"> </SPAN>set to "Clustal characters" are those in which the two sequences<SPAN class="Apple-converted-space"> </SPAN>differ.<SPAN class="Apple-converted-space"> </SPAN>That is the closest I can get to your request,<SPAN class="Apple-converted-space"> </SPAN>unfortunately.<SPAN class="Apple-converted-space"> </SPAN>There is a format of input that lets you color rows<SPAN class="Apple-converted-space"> </SPAN>and columns in the alignment, but then you'd have to calculate<SPAN class="Apple-converted-space"> </SPAN>yourself which positions had differing residues and then write out<SPAN class="Apple-converted-space"> </SPAN>such a file.<SPAN class="Apple-converted-space"> </SPAN>Maybe too bothersome to be worth it.<SPAN class="Apple-converted-space"> </SPAN>Such a file is<SPAN class="Apple-converted-space"> </SPAN>loaded into Multalign Viewer using "Tools... Load SCF/Seqsel File"<SPAN class="Apple-converted-space"> </SPAN>and the file format is described in:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/</A> multalignviewer/jevtrace.html</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Coming soon:<SPAN class="Apple-converted-space"> </SPAN>we just added more and fancier options for<SPAN class="Apple-converted-space"> </SPAN>"Conservation style" which, although they do not address your<SPAN class="Apple-converted-space"> </SPAN>specific question in this mail, might interest you:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/</A> multalignviewer/multalignviewer.html#mavpref-analysis</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">(development documentation; we don't have a release with these<SPAN class="Apple-converted-space"> </SPAN>features yet)</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Best,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Elaine</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">-----</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Elaine C. Meng, Ph.D.<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">UCSF Computer Graphics Lab and Babbitt Lab</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Department of Pharmaceutical Chemistry</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of California, San Francisco</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN><A href="http://www.cgl.ucsf.edu/home/meng/index.html">http://www.cgl.ucsf.edu/home/meng/index.html</A></DIV> <BR></BLOCKQUOTE><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chimera-users mailing list</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</A></DIV> <BR class="Apple-interchange-newline"></BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>