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<p class="MsoNormal"><span lang="EN-US">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">I tried to fit some models into a large density map using python script for chimera.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Do you know how to set the VolumeViewer module in python script to show all the surface of the density map like command line”</span></p>
<p class="MsoNormal"><i>volume #1 style surface region all level 0.15 step 1</i><span lang="EN-US">”?
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Here is my python code:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Import chimera<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">import FitMap<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">import VolumeViewer<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">model_list = chimera.openModels.open("test.pdb")<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">em_map = VolumeViewer.open_volume_file("test.mrc")[0]<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US">“python code ” for “</span><i>volume #1 style surface region all level 0.15 step 1</i></b><b><span lang="EN-US">”<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span lang="EN-US"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span lang="EN-US">model = chimera.selection.ItemizedSelection([model_list[0]])<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">listfit = FitMap.fitcmd.fitmap(model, em_map, resolution=5.0, metric="correlation")<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thanks and best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Yumeng<o:p></o:p></span></p>
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