[Chimera-users] Place Objects output to mrc

Pranav Shah p.shah.lab at gmail.com
Fri May 20 08:57:36 PDT 2022

Thanks Ricardo!
Pranav Shah
Postdoctoral Research Fellow.

Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive, Oxford OX3 7BN,

On Fri, May 20, 2022 at 3:31 PM Ricardo Righetto
<ricardorighetto at gmail.com> wrote:
> Hi,
> Regarding https://www.rbvi.ucsf.edu/pipermail/chimera-users/2022-March/018516.html
> I stumbled upon this thread somewhat late, so here is my approach to do what Pranav asked, just in case:
> 1. Use the "Place Objects" plugin to map back your particles into the tomogram, using STL files to represent the average
> 2. Generate an MRC volume made up entirely of "ones", exactly the same size as your tomogram. For example, for a volume that is 928x928x464 voxels one can do this in EMAN using:
> $ e2proc3d.py :928:928:464:1 ones_bin4.mrc
> You could obviously use some other program to do the same thing, or Python, MATLAB, etc.
> 3. Load this "ones" volume in your Chimera session. Make sure all regions are loaded in step 1, e.g.
> vol #2 style surface step 1 level 0.5 region all
> (the volume doesn't have to be visible, though)
> 4. Mask your "ones" volume using the surface of the mapbacks from "Place Object", e.g.:
> mask #1 #2 fullmap true
> 5. Save the new, masked volume as an MRC file
> The result is essentially a binary volume (well, not exactly because of the masking interpolation) where voxels of your mapped-back particles are 1 and the rest is 0. This is quite useful to compose segmentations and mapbacks on tomograms in Chimera or ChimeraX having full control like we do with any MRC volume (unlike e.g. STL or COLLADA objects).
> Note you may get some artifacts on the edges, so you might have to play a bit with the thresholds both when creating the STL of your subtomogram average and when displaying your new volume "sculpted" by the mapbacks, to minimize those. The results however have been good enough in my experience, working with low-resolution averages :-)
> Hope this helps!
> Best wishes,
> --
> Ricardo Diogo Righetto

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