[Chimera-users] Finding dimensions of density map

[Ryan Harlich]

Hi Elaine,



I decided to give the meshmol a try but cannot save. Get error “No models chosen to save” and I have mesh density.mrc (#1) selected.



Best,

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.

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>

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

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/meshmol.html>

then,
… 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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