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Imod uses nanometers as its base spatial unit. The files are aligned in imod. Looks like a fix in the chimera reader is needed to fix scale. My next test here is to set the scaling 10x higher in imod and see what happens to the origin. Desirable to have the
MRC and imod file open correctly in chimera, would be the default expectation.<br>
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The IMOD file I am using is 350MB. MRC is 500 MB.<br>
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The easiest route to separate the segmentation is multiple imod files, unless it overloads chimera. Another possibility would be to get the segmented density and import that into chimera, which might be best strategy by allowing volume rendering control and
better performance. Not familiar with imod, need to read the documentation.<br>
<br>
Matthew Dougherty<br>
National Center for Macromolecular Imaging<br>
Baylor College of Medicine<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Monday, May 4, 2015 12:24:02 PM<br>
<b>To:</b> Dougherty, Matthew T<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] imod</font>
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<div>Hi Matt,
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<div class=""> Sounds like the IMOD segmentation is using units of nanometers while the MRC map uses Angstroms. I don’t know if the IMOD segmentation tool uses the mrc file origin — if not, that could explain why you need to use origin 0,0,0 in Chimera to
align. Does this IMOD segmentation file and MRC map file align when opened with IMOD? When you open the segmentation in Chimera (*.imod file) it will report the pixel size and scale that it read from the IMOD header in the Chimera Reply Log, e.g.</div>
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<div class="">IMOD pixel size = 22.55 scale (1.0, 1.0, 1.0)</div>
<div class="">ctl.imod mesh opened</div>
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<div class=""> Chimera has no way to reduce the level of detail in an IMOD mesh to make the graphics go faster. It usually takes more than 10 million triangles to slow down a modern graphics card, and that would take an IMOD file at least a few hundred Mbytes
in size. Is your file that large?</div>
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<div class=""> You can split a surface so that each of its connected components can be individually selected using</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>sop split #0</div>
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<div class="">where #0 is the surface model you want to split.</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span><a href="http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sop.html" class="">http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/sop.html</a></div>
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<div class="">But after you split it Chimera no longer knows that all the microtubules belong to one group. Also this sop split creates a new split model and hides the original surfaces. Reshowing the original surfaces requires “sop show #0”.</div>
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom</div>
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<blockquote type="cite" class="">
<div class="">On May 1, 2015, at 2:28 PM, Dougherty, Matthew T wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I have recently been getting some imod segmentation files and have been noticing three problems<br class="">
</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">1) when I read the MRC and imod files I am having a scaling problem, and the datasets do not integrate.<br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">For example, if the MRC voxel size is 31.22 31.22 31.22, and the origin index is 0 -114 0, I have to change the the voxel size to<span class="Apple-converted-space"> </span><span style="font-size: 12pt;" class="">3.122 </span>3.122 3.122
, and the origin index to <span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">0 0 0 so that graphics match correctly. Since there are number of people in the data chain before it
gets to me, I thought it might check to determine if this is known problem before going upstream to unknown people to figure out if they are getting the imod output settings correct.</span><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class=""><br class="">
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class=""><br class="">
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">2) The graphics performance with imod segmentation files is sluggish
in chimera, not sure what it is in imod. I assume that the format defines the vertices at the highest resolution corresponding with the MRC file. Is there a way to improve the performance on the chimera side? I am not using contouring, just reading the file
in default mode.</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class=""><br class="">
</span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-family: Calibri, Arial, Helvetica, sans-serif; font-size: 16px; background-color: rgb(255, 255, 255);" class="">3) The segmentation has a lot of components, such as vesicles and microtubules,
that have different colors. Is there a way to break apart the components so they can be manipulated seperately? E.g., display/hide, change colors, translate and rotate.</span></div>
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<div id="Signature" class="">
<div class="BodyFragment"><font size="2" class="">
<div class="PlainText">Matthew Dougherty<br class="">
National Center for Macromolecular Imaging<br class="">
Baylor College of Medicine<br class="">
===========================================================================</div>
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