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<p class="MsoNormal">I tried doing what you suggested and not sure how voxel size and origin will give you the bounding box. The other suggestion I am not sure if you understood what I am trying to accomplish or I did not understand what you were suggesting.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I am basically trying to get the bounding box. I tried with one atom and its bounding box would be small so what I did cut my volume. So I thought instead of one atom I can get eight atoms in all corners so when I resample it does not cut
any of my volume because of the bounding box. I also want the biggest bounding box of two volumes.</p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,</p>
<p class="MsoNormal">Ryan Harlich</p>
<p class="MsoNormal"><o:p> </o:p></p>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Ryan Harlich<br>
<b>Sent:</b> Thursday, July 11, 2019 1:29:22 PM<br>
<b>To:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> RE: [Chimera-users] Finding dimensions of density map</font>
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<p class="x_MsoNormal">Hi Elaine,</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">I am doing it no GUI via command line so I cannot select with mouse.</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">Thanks,</p>
<p class="x_MsoNormal">Ryan Harlich</p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Sent:</b> Thursday, July 11, 2019 12:49:19 PM<br>
<b>To:</b> Ryan Harlich<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Finding dimensions of density map</font>
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<div class="PlainText">Hi Ryan,<br>
The “Coordinates” section of Volume Viewer (open from its Features menu) gives values used to convert between the dataset grid and Cartesian coordinates. You’d have to back-calculate from the origin index and voxel size.<br>
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html</a>><br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates</a>><br>
<br>
Another approach might be to show the volume outline box and then use the “meshmol” command to make it into a (pseudo)atomic model. That will also make the volume isosurface triangles into atoms, but you can select just the box part and write selected-only
as a PDB file. E.g. if the volume model is #4, command:<br>
<br>
meshmol #4 1<br>
<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html">http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html</a>><br>
<br>
then,<br>
… Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box<br>
...use “write” command or File… Save PDB with their respective option to save only the selected part<br>
<br>
I hope this helps,<br>
Chimera ;-)<br>
-----<br>
Elaine C. Meng, Ph.D.<br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich@hotmail.com> wrote:<br>
> <br>
> Hi Chimera,<br>
> <br>
> I want to plot 8 voxels (atoms) in a pdb such that they are the slightly greater than the greatest bounding box of two mrc density maps. In order to do that I need the dimensions of both mrc density maps or there eight greatest corners. How would I go about
doing this; that is, getting the 8 corners of the mrc density maps? Is there a command to help this process?<br>
> <br>
> Best,<br>
> Ryan Harlich<br>
<br>
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