<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Thanks for the quick replay! </div><div>But my case is that no homology model for the target protein and it should be built directly from the em map. What should I do in this case ?</div><div><br></div><div><br></div><div><br></div><div><br></div><div style="position:relative;zoom:1">--<br><div><font face="Helvetica, Microsoft Yahei, verdana">Wei Ding</font></div><div><span style="line-height: 23.8px;">P.O.Box 603</span></div><div>The Institute of Physics,<span style="line-height: 1.7;">Chinese Academy of Sciences</span></div><div>Beijing,<span style="line-height: 1.7;">China</span></div><div><span style="line-height: 23.8px;">100190</span></div><span style="font-family: Helvetica, 'Microsoft Yahei', verdana; ">Tel: +86-10-82649083</span><br style="font-family: Helvetica, 'Microsoft Yahei', verdana; "><span style="font-family: Helvetica, 'Microsoft Yahei', verdana; ">E-mail: dingwei</span><a href="mailto:wangli@moon.ibp.ac.cn" target="_blank" style="color: rgb(0, 51, 153); font-family: Helvetica, 'Microsoft Yahei', verdana; ">@iphy.ac.cn</a><div style="clear:both"></div></div><div id="divNeteaseMailCard"></div><div><br></div>At 2018-12-29 15:30:51, "Pavel Afonine" <pafonine@lbl.gov> wrote:<br> <blockquote id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
Hi Wei,<br>
<br>
cutting out a box with model and map around it may be a solution for
your case. A tool for this is phenix.map_box or its GUI equivalent.<br>
<br>
Pavel<br>
<br>
P.S.: phenix.real_space_refine does this internally so 'irrelevant'
box size never affects runtime of refinement.<br>
<br>
<br>
<div class="moz-cite-prefix">On 12/28/18 23:14, <a class="moz-txt-link-abbreviated" href="mailto:dancingdream@163.com">dancingdream@163.com</a>
wrote:<br>
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<blockquote type="cite" cite="mid:3cff69db.8eac.167f8d069cd.Coremail.dancingdream@163.com">
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<div><span style="font-size: 18px;">Dear all,</span></div>
<div><span style="font-size: 18px;">The cell parameter of the EM
map is always too large, which will make the model building
program running very slow.</span></div>
<div><span style="font-size: 18px;">But in factor, the structure
is a smal part of cell. So can I smaller the cell parameter
when I use <span style="font-size: 18px; font-family:
Menlo;">phenix.map_to_structure_factors to convert the EM
map to </span></span><font face="Menlo" size="4"><span style="font-size: 18px;">mtz file.</span></font></div>
<div><font face="Menlo" size="4"><span style="font-size: 18px;">Thank
a lot!</span></font></div>
<div><font face="Menlo" size="4"><br>
</font></div>
<div><font face="Menlo" size="4">Wei</font></div>
<div><br>
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