Hi Bodvael,<br><br>Please check out my answer in blue color for your query. <br><br><div style="text-align:left">I have never used Chimera so please bear with me. I have this short 
peptide sequence (8 aa) that I want to locate in the secondary structure
 of a protein which I have opened in chimera. Is there a way to 
highlight the sequence in a particular color in the 3D model and/or only
 have the aminoacid numbering in this region?<br><font size="6"><i style="font-family:comic sans ms,sans-serif"><font style="color:rgb(0, 0, 153)"></font></i></font><br><span style="color: rgb(0, 0, 153);">Yes, you can highlight the desired region using Chimera. After loading your structure, goto</span><br style="color: rgb(0, 0, 153);">
<span style="color: rgb(0, 0, 153);"> </span><br style="color: rgb(0, 0, 153);"><div style="text-align: center;"><b style="color: rgb(0, 0, 153);">Tools -&gt; Sequence -&gt; Sequence </b><br style="color: rgb(0, 0, 153);">
<br style="color: rgb(0, 0, 153);"><div style="text-align: left;"><span style="color: rgb(0, 0, 153);">to display the sequence. Here, you can find that by default, alpha - helices are highlighted in yellow, sheets in green in the sequence window. Now, to highlight the region of your interest, just drag on the residues that you want. You can see that the residues you have selected are highlighted in green in the structure window. Now goto </span><br style="color: rgb(0, 0, 153);">
<div style="text-align: center;"><b><span style="color: rgb(0, 0, 153);">Actions -&gt; Color -&gt; choose a color of your choice</span><br><br></b><div style="text-align: left; color: rgb(0, 0, 153);">To have the amino acid numbering, <span style="color: rgb(0, 0, 153);">goto </span><b><span style="color: rgb(0, 0, 153);"><br>
<br>Actions -&gt; Label -&gt; Residue -&gt; Specifier (you can select 1-letter code + specifier to have the amino acid residue and residue number labelled). </span><br></b></div></div></div></div><br><br>I have never used Chimera so please bear with me. I have this short 
peptide sequence (8 aa) that I want to locate in the secondary structure
 of a protein which I have opened in chimera. Is there a way to 
highlight the sequence in a particular color in the 3D model and/or only
 have the aminoacid numbering in this region?<br><br style="color: rgb(0, 0, 153);"><span style="color: rgb(0, 0, 153);">I am unsure, if you can display the strand numbers in Chimera. The best way is to identify the N- and C- terminal and count the strand from N- terminal. <br>
<b style="color: rgb(0, 0, 0);"><br>-Suda </b><br></span></div><br>
<br><br><div class="gmail_quote">On Tue, Nov 15, 2011 at 7:12 AM, bodvael email <span dir="ltr">&lt;<a href="mailto:bodvael@gmail.com">bodvael@gmail.com</a>&gt;</span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div>Hi,</div><div> </div><div>I have never used Chimera so please bear with me. I have this short peptide sequence (8 aa) that I want to locate in the secondary structure of a protein which I have opened in chimera. Is there a way to highlight the sequence in a particular color in the 3D model and/or only have the aminoacid numbering in this region?</div>


<div> </div><div>Also, I would like to view a linear alignment of the entire protein sequence with my peptide sequence of interest. I was able to do that and see that the peptide sequence falls in a beta-sheet (green color). Is there any way know which strand it is exactly? It is supposed to be in strand 5 but I don&#39;t know how to display strand numbers, or verify with certainty that it is indeed strand 5 and not strand 6 for example.</div>


<div> </div><div>Thanks,</div><div>Bodvael</div>
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