<html><body bgcolor="#FFFFFF"><div>Hi</div><div><br></div><div>Often in such cases the signal is relatively weak for the second domain, especially at the rotation function step. There are two main things we recommend (which you may have tried). First, lower the threshold for peaks in the rotation search from the default of 75% of maximum to, say, 50%. It may also help to turn off the clustering of rotation peaks. Second, take advantage of anything you might know about the orientation of the second domain. If you have another structure with the same pair of domains their relative orientation is likely to be similar, so you can use a "rotate around" search to restrict the relative orientation within, say, 30 degrees of the first.</div><div><br></div><div>Regards</div><div><br></div><div>Randy Read<br><br>----<br><div><div>Randy J. Read</div></div></div><div><br>On 22 Aug 2011, at 08:12, intekhab alam <<a href="mailto:faisaldbg@gmail.com">faisaldbg@gmail.com</a>> wrote:<br><br></div><div></div><blockquote type="cite"><div><div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">Hi there </font></span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">I have a data of heterotrimer protein complex at 2.9A resolution.</font></span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">One protein consists of two domains. I tried phaser as well as molrep which gives a solution with only one domain.</font></span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">Rotation function and translation function were found to be fine for these solutions.</font></span></p></font></span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">I tried to find missing domain of the protein after fixing one of the domain or the other partner proteins using whole part or various truncations of missing domain.</font></span></p>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">I also tried to find and build missing domain using Rosetta with the solutions of Molrep or Phaser as template.</font></span></p></font></span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">But, there were no solutions, or the solutions are clashed with other domain or proteins. </font></span></div>
<p style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">Furthermore, R and Rfree is 30 and 40, respectively, and I could not reduce them further.</font></span></p>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">There was almost no electron density map in the empty space so that I could not model manually.</font></span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕"></font></span> </div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">Plz guide me ,how can i look for the missing domain in the protein.</font></span></div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕"></font></span> </div>
<div style="MARGIN: 0cm 0cm 0pt" class="MsoNormal"><span lang="EN-US"><font face="맑은 고딕">regards</font></span></div><br clear="all"><br clear="all"><br>-- <br>INTEKHAB ALAM<br>LABORATORY OF STRUCTURAL BIOINFORMATICS<br>KOREA UNIVERSITY, SEOUL<br>
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