[Chimera-users] generating/saving mask files using segmentation

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 19 12:07:38 PST 2018

Hi Uhnsoo,
Welcome to Chimera!

I’m guessing you used the Segment Map tool for segmenting.  You’re right, it does make a smaller box for each region when you save them from the Segment Map “File” menu.  After saving the segmented regions, you can resample them to the grid of the original map to make additional copies of the maps with the full box size.

For example, I had a map #0.1 that I segmented into 3 regions with Segment Map, and saved as new maps #2-4 with smaller boxes.  Then to make additional copies of these maps with the original-size box in the original position, used command “vop resample”:

vop resample #3 on #0.1
vop resample #3 on #0.1
vop resample #4 on #0.1

This created additional maps #5-7 with “resampled” in their names.  The command has other possible options, see:

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

> On Nov 18, 2018, at 4:18 PM, Uhnsoo Cho <ecoli72 at gmail.com> wrote:
> Hi,
> I am a beginner and still in the learning phase of chimera. 
> Here is my question.
> I generated the mask from relion (mask creation) and open the mask in chimera.
> Using segmentation, I successfully split the mask into three segments and saved them individually.
> Then, I found that each mask file changes its box size (smaller than the original mask) and failed to run the multi-body refinement in relion.
> Using relion_image_handler (--new_box), I changed the box size but now the origin is shifted and all three masks are overlapping each other by losing their relative position.
> Is there a way to save the segmented mask maps by maintaining its original box size and relative position?
> Thanks.
> Best, Uhnsoo 

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