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Hi,<br>
<br>
I can try to help if you send me the Fobs data and current model.
Plus, tell me the coordinates of two anchor points marking the start
and the end of the segment that you want to build, and the sequence
that is supposed to be in-between these anchor point. The I can try
using my tool (that I'm still developping) to build that segment
from scratch into whatever map you have. This tool is not picky
about map quality and builds things in seconds.<br>
<br>
Pavel<br>
<br>
<br>
On 2/8/12 11:15 PM, intekhab alam wrote:
<blockquote
cite="mid:CA+-VYKWz82gJuuc6AAxC_MdOfyh8eeU1MzjQZuijyTg1hQoFPQ@mail.gmail.com"
type="cite">
<div>Hi all</div>
<div>I have a 3A dataset for a protein-protein complex. I have
successfully build the first protein and refined it to R/Rfree
24/28. I can see some density for my second protein but the
density is a bit noisy. I have attached the coot image of the
density. I want to model the aminoacid having sequence as
given </div>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><span style=""
lang="EN-US">peptide:</span></p>
<p style="MARGIN:0cm 0cm 0pt" class="MsoNormal"><font
color="#ff6666"><span style="" lang="EN-US">MGKKGKNKKG</span><span
style="" lang="EN-US">R</span><span style="" lang="EN-US">G</span><span
style="" lang="EN-US">R</span><span style="" lang="EN-US">PGVF</span><span
style="" lang="EN-US">R</span><span style="" lang="EN-US">T</span><span
style="" lang="EN-US">R</span><span style="" lang="EN-US">G</span><span
style="" lang="EN-US">LTDEEYDEFKK</span><span style=""
lang="EN-US">RR</span><span style="" lang="EN-US">ES</span><span
style="" lang="EN-US">R</span><span style="" lang="EN-US">GGKYSIDDYLAD</span><span
style="" lang="EN-US">R</span><span style="" lang="EN-US">E</span><span
style="" lang="EN-US">R</span><span style="" lang="EN-US">EEELLE</span><span
style="" lang="EN-US">R</span><span style="" lang="EN-US">DEEEAIFGDGFGLE</span></font></p>
<div><br clear="all">
1.Based on map features which segemnt should i start with.</div>
<div>2. Is there anyway that i can build the best fit segment of
my second protein. <br>
</div>
<div>I tried autobuild but it failed to build any peptide for my
second protein.</div>
<div> </div>
<div>Your help is highly appreciated.</div>
<div> </div>
<div>regards</div>
<div> </div>
<div>-- </div>
<div><br>
INTEKHAB ALAM<br>
LABORATORY OF STRUCTURAL BIOINFORMATICS<br>
KOREA UNIVERSITY, SEOUL<br>
</div>
<br>
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