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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi, Tom,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Sorry to bother you again. When I run the code you shared with me in the following (I modified it a little bit),<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">+++++++++++++++++++++++++++++++++++++++++++++++<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">import sys, getopt<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">sys.path.insert(0, '/home/rli/.local/UCSF-Chimera64-1.10.2 /lib')<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">from _chimera import OpenModels<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">m = OpenModels.open('1a0m', 'PDB')[0] # Open atomic model<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">v = OpenModels.open('1a0m', 'EDSID')[0] # Open xray density map, #1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">for a in m.atoms:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> xyz = a.coord().data()<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> i,j,k = v.data.xyz_to_ijk(xyz)<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:9.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">print 'Atom %s is at grid point %.1f, %.1f, %.1f' % (a.oslIdent(), i, j, k)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:9.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-indent:9.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I got such an error:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-------------------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:9.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:9.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> File "atomgrid.py", line 8, in <module><o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:9.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> m = OpenModels.open('1a0m', 'PDB')[0] # Open atomic model<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:9.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">AttributeError: type object '_chimera.OpenModels' has no attribute 'open'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-----------------------------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:9.0pt"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I don’t know which part I did is wrong. Thank you very much for your help again.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Rongjian<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> Tom Goddard [mailto:goddard@sonic.net]
<br>
<b>Sent:</b> Thursday, February 11, 2016 5:42 PM<br>
<b>To:</b> rongjian li<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] mapping between MRC and PDB<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Rongjian,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Here is some python that you can open in Chimera (File / Open) that will load an atomic model (PDB 1a0m) and density map (x-ray map for 1a0m) and print the density map grid index of each atom. The index is floating point since the atoms
of course are not exactly at grid points.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> The Chimera Python scripts web page has more example code<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span><a href="http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts">http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Tom<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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