<div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial"><div>Perfect!&nbsp;This problem bothering me for so long was finally solved!&nbsp;</div><div>Thank you very much for your help!</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:&nbsp;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> 2018-12-30 00:43:01"Pavel Afonine" &lt;pafonine@lbl.gov&gt; д<br> <blockquote id="isReplyContent" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
  
    
  
  
    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">
      
      <div style="line-height:1.7;color:#000000;font-size:14px;font-family:Arial">
        <div>Thanks for the quick replay!&nbsp;</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:&nbsp;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">&lt;pafonine@lbl.gov&gt;</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&nbsp;<span style="font-size:
                    18px; font-family: Menlo;">phenix.map_to_structure_factors
                    to convert the EM map to&nbsp;</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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