<html><head><style data-externalstyle="true">
p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph {
margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.5in;
margin-bottom:.0001pt;
}

p.MsoListParagraphCxSpFirst, li.MsoListParagraphCxSpFirst, div.MsoListParagraphCxSpFirst, p.MsoListParagraphCxSpMiddle, li.MsoListParagraphCxSpMiddle, div.MsoListParagraphCxSpMiddle, p.MsoListParagraphCxSpLast, li.MsoListParagraphCxSpLast, div.MsoListParagraphCxSpLast {
margin-top:0in;
margin-right:0in;
margin-bottom:0in;
margin-left:.5in;
margin-bottom:.0001pt;
line-height:115%;
}
</style><style><!--
.EmailQuote {
padding-left:4pt;
margin-left:1pt;
border-left-color:rgb(128, 0, 0);
border-left-width:2px;
border-left-style:solid;
}
--></style></head><body><div data-externalstyle="false" style="font-family:Calibri,'Segoe UI',Meiryo,'Microsoft YaHei UI','Microsoft JhengHei UI','Malgun Gothic','Khmer UI','Nirmala UI',Tunga,'Lao UI',Ebrima,sans-serif;font-size:16px;"><div>Hi,</div><div data-focusfrompointer="true">It works perfectly, thank you for helping me. </div><div data-focusfrompointer="true">Best regards,</div><div data-focusfrompointer="true">Nadia</div><div data-signatureblock="true"><div data-focusfrompointer="true">&nbsp;</div><div>Sent from Windows Mail</div><div data-focusfrompointer="true">&nbsp;</div></div>        <div style="border-top-color: rgb(225, 225, 225); border-top-width: 1px; border-top-style: solid;">                <strong>From:</strong>&nbsp;Elaine Meng<br>                <strong>Sent:</strong>&nbsp;‎February‎ ‎8‎, ‎2015 ‎12‎:‎52‎ ‎AM<br>                <strong>To:</strong>&nbsp;Nadia Raboana<br>                        <strong>CC:</strong>&nbsp;chimera-users@cgl.ucsf.edu<br>                <strong>Subject:</strong>&nbsp;Re: [Chimera-users] Ramachandran plot statistics<br>        </div>        <div>&nbsp;</div>




<div class=" PlainText" data-focusfrompointer="true">Hi Nadia,<br>
You would have to decide for yourself what probability cutoff you want to use as the boundary between allowed and disallowed.<br>
<br>
First assign the probabilities to the residues:&nbsp; in the Ramachandran Plot dialog, click the button at the bottom to “Assign Residue Probabilities” (or use the ramachandran command option “assign”):<br>
&lt;<a tabindex="-1" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ramachandran/ramachandran.html</a>&gt;<br>
&lt;<a tabindex="-1" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ramachandran.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/ramachandran.html</a>&gt;<br>
<br>
Then in Select by Attribute (Chimera menu: Select… By Attribute Value) choose attributes of “residues” with Attribute: ramaProb … that will show a histogram of the probability values.&nbsp; Then you can move the green bars to enclose the range of probabilities you want to select.&nbsp; After you use that dialog to select everything above your cutoff probability, then you can get a count of the selected residues by clicking the green magnifying glass at the bottom right corner of the Chimera window to show the Selection Inspector.<br>
&lt;<a tabindex="-1" href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html#select</a>&gt;<br>
&lt;<a tabindex="-1" href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html</a>&gt;<br>
<br>
Then you would divide by the total number of amino acid residues to get the percentage.&nbsp; You could count the total number of amino acid residues, for example, by using command “select protein” and then clicking the green magnifying glass.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
On Feb 7, 2015, at 4:49 AM, Nadia Raboana &lt;nadia_raboana@hotmail.fr&gt; wrote:<br>
<br>
&gt; Hello,<br>
&gt; I am using UCSF Chimera to generate Ramachandran plot related to my protein structure. I would like to know how to get the statistics about the analysis. I would precisely know the percentage values of residues in most favored regions, allowed regions and disallowed regions.<br>
&gt; Thank you for answering me.<br>
&gt; Best regards,<br>
&gt; Nadia Raboanatahiry<br>
<br>
</div>


</div></body></html>