[Chimera-users] How to fix .mrc file opening to a very small size?

[Elaine Meng]

Hi Ahmad,
You can see the current outline box (which probably contains a lot of empty space) with command: 
volume all showoutline true
(it’s also in the Volume Viewer dialog, menu: Features… Data display options)

To crop to a smaller box and save only that, you can draw the smaller box manually. To do that, choose Volume Viewer menu: Features... Subregion selection, and turn on the option to “Select subregions using” your mouse button of choice.  More details on how to use the mouse to draw a box:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#mouseselect>

Once you have the box drawn how you like, click the Crop button in Volume Viewer (right under “Select subregions…) and then use Volume Viewer menu: "File… Save map as” to save that smaller-boxed map as a new file.

Then when you close everything and then open the new map, it will be zoomed in more on the density.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 14, 2018, at 3:11 PM, Ahmad Abdelzaher <underoath006 at gmail.com> wrote:
> 
> Someone shared a density map with me. I'm not sure how they "cropped" that particular density, but the file they sent me is huge in size, and contains only a small density that I have to zoom in and adjust every time I open the .mrc file.
> 
> How can I fix it? 
> 
> Regards.