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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">Thank you so much for your patient reply.<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">May I ask, is there any example code in Python, like you suggested, so that I could know how to run it more clearly? <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">Thanks 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>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><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]
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<b>Sent:</b> Thursday, February 11, 2016 4:56 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"> The volume rotation angle is almost always zero so the rotation axis does not effect the relation between grid indices and x,y,z positions in space. If you are working with x-ray crystallography maps, the cell angles will often not be
90 degrees, meaning that the rectangular box bounding the density map is skewed — you would have to use that.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> If you are writing a script in Python within Chimera you can directly access the mapping of grid index positions to x,y,z positions in the scene (ie atomic coordinates) using<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>p = (12.34, -1.58, 27.7)<o:p></o:p></p>
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<p class="MsoNormal"><span class="apple-tab-span"> </span>i,j,k = v.data.xyz_to_ijk(p)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">where v is a Volume model. The v.data is a Grid_Data object which is defined in Python by the following 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/browser/trunk/libs/VolumeData/griddata.py">http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/VolumeData/griddata.py</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">which is part of your Chimera distribution in<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>chimera/share/VolumeData/griddata.py<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">or on Mac<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>Chimera.app/Contents/Resources/share/VolumeData/griddata.py<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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<p class="MsoNormal">On Feb 11, 2016, at 2:23 PM, rongjian li wrote:<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 style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Hi,<span class="apple-converted-space"> </span><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am a beginner in using Chimera. I have a simple question for you experts and I really appreciate any guide for me.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am working on a project needs to create a one-to-one mapping between MRC grid and PDB atoms. For example, from the PDB file, I know the physical coordinates of each atom.
I want to know whether each atom is out of the 3D volume of MRC or not. If it is inside the volume, I hope to know which voxel grid this atom is in.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I have figured out the mapping between the physical origin of PDB system and its grid index in MRC using Chimera Volume Viewer -- > Features ---> Coordinates ----> Origin
Index. But I am not sure whether the information of ‘Rotation axis’ is also very important, which is usually [0,0,1] in Chimera Volume Viewer -- > Features ---> Coordinates ----> Rotation axis. <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Thank you very much.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Best,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Rongjian<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
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Manage subscription:<span class="apple-converted-space"> </span></span><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";color:purple">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</span></a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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