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<p class="x_MsoNormal">Hi Elaine,</p>
<p class="x_MsoNormal"> </p>
<p class="x_MsoNormal">One if fine. But is there a way to do it without the GUI? The method you suggest required me to hand select the corners. I am writing a Python program so I am using --nogui.</p>
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<p class="x_MsoNormal">Best,</p>
<p class="x_MsoNormal">Ryan Harlich</p>
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<p class="x_MsoNormal">Sent from <a href="https://go.microsoft.com/fwlink/?LinkId=550986">
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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> Friday, July 12, 2019 9:22:38 AM<br>
<b>To:</b> Ryan Harlich<br>
<b>Cc:</b> chimera-users@cgl.ucsf.edu BB<br>
<b>Subject:</b> Re: [Chimera-users] Finding dimensions of density map</font>
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<div class="PlainText">Hi Ryan,<br>
I think I did understood you: My suggestion to save the volume outline box as a molecule would give you 8 atoms at the corners, in PDB format. However, there is no similar thing to get a collective bounding box for multiple datasets. You’d just have to get
a box for each volume data set and then figure out for yourself the min and max in each dimension among all the boxes. As Tom G said, if this is something you want to do repeatedly, python scripting may be the only reasonable approach.<br>
Elaine<br>
<br>
> On Jul 11, 2019, at 4:05 PM, Ryan Harlich <ryanharlich@hotmail.com> wrote:<br>
> <br>
> 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.<br>
> <br>
> 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.<br>
> <br>
> Best,<br>
> Ryan Harlich<br>
> <br>
> Sent from Mail for Windows 10<br>
> <br>
> From: Ryan Harlich<br>
> Sent: Thursday, July 11, 2019 1:29:22 PM<br>
> To: chimera-users@cgl.ucsf.edu BB<br>
> Subject: RE: [Chimera-users] Finding dimensions of density map<br>
> <br>
> Hi Elaine,<br>
> <br>
> I am doing it no GUI via command line so I cannot select with mouse.<br>
> <br>
> Thanks,<br>
> Ryan Harlich<br>
> <br>
> Sent from Mail for Windows 10<br>
> <br>
> From: Elaine Meng <meng@cgl.ucsf.edu><br>
> Sent: Thursday, July 11, 2019 12:49:19 PM<br>
> To: Ryan Harlich<br>
> Cc: chimera-users@cgl.ucsf.edu<br>
> Subject: Re: [Chimera-users] Finding dimensions of density map<br>
> <br>
> 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="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=qLa0zvb7%2F9qeEOWFk%2BZfEJHi%2FBAhyCPi07BJf0LuRRA%3D&reserved=0">https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fframevolumeviewer.html&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=qLa0zvb7%2F9qeEOWFk%2BZfEJHi%2FBAhyCPi07BJf0LuRRA%3D&reserved=0</a>><br>
> <<a href="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=fxqKjEiOqwrZJAlgyvOXl8iJrLQ0Juc8o2ZiVLVgP98%3D&reserved=0">https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FContributedSoftware%2Fvolumeviewer%2Fvolumeviewer.html%23coordinates&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641017361&sdata=fxqKjEiOqwrZJAlgyvOXl8iJrLQ0Juc8o2ZiVLVgP98%3D&reserved=0</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="https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fmeshmol.html&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641027366&sdata=LAs5XM%2BXu%2BOGFXKxu7Z5MwqXkmMZPZe9GhBfLCBn2WA%3D&reserved=0">https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimera%2Fdocs%2FUsersGuide%2Fmidas%2Fmeshmol.html&data=02%7C01%7C%7C377fb79ae7e4401ad7b708d706e529ac%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636985453641027366&sdata=LAs5XM%2BXu%2BOGFXKxu7Z5MwqXkmMZPZe9GhBfLCBn2WA%3D&reserved=0</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>
> _______________________________________________<br>
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