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Hi,<br>
<br>
have a look at the documentation:<br>
<br>
<a class="moz-txt-link-freetext" href="https://www.phenix-online.org/documentation/reference/map_box.html">https://www.phenix-online.org/documentation/reference/map_box.html</a><br>
<br>
Reading through it I find this<br>
<br>
phenix.map_box map.mrc density_select=true<br>
<br>
should do it. Let us know if it doesn't.<br>
<br>
Pavel<br>
<br>
<div class="moz-cite-prefix">On 12/29/18 07:46, <a class="moz-txt-link-abbreviated" href="mailto:dancingdream@163.com">dancingdream@163.com</a>
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:38d221bb.ed71.167faa54b0e.Coremail.dancingdream@163.com">
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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; " moz-do-not-send="true">@iphy.ac.cn</a></div>
<div><br>
</div>
At 2018-12-29 15:30:51, "Pavel Afonine" <a class="moz-txt-link-rfc2396E" href="mailto:pafonine@lbl.gov"><pafonine@lbl.gov></a>
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" moz-do-not-send="true">dancingdream@163.com</a>
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:3cff69db.8eac.167f8d069cd.Coremail.dancingdream@163.com">
<div
style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
<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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