[Chimera-users] Finding dimensions of density map

Ryan Harlich ryanharlich at hotmail.com
Thu Jul 11 16:05:00 PDT 2019

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.

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.

Ryan Harlich

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From: Ryan Harlich
Sent: Thursday, July 11, 2019 1:29:22 PM
To: chimera-users at cgl.ucsf.edu BB
Subject: RE: [Chimera-users] Finding dimensions of density map

Hi Elaine,

I am doing it no GUI via command line so I cannot select with mouse.


Ryan Harlich

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From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Thursday, July 11, 2019 12:49:19 PM
To: Ryan Harlich
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Finding dimensions of density map

Hi Ryan,
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.


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:

meshmol #4 1


… Ctrl-click on one corner of box to select atom, press up arrow one time to promote to whole box
...use “write” command or File… Save PDB with their respective option to save only the selected part

I hope this helps,
Chimera  ;-)
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jul 11, 2019, at 10:57 AM, Ryan Harlich <ryanharlich at hotmail.com> wrote:
> Hi Chimera,
> 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?
> Best,
> Ryan Harlich

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