[Chimera-users] Questions about IMOD files in Chimera software.

[Elaine Meng]

Dear Si Hoon Park,
That's a lot of questions!  I will try to number them separately.

(1) Chimera can read some IMOD file types.  Here is the list of the file types Chimera can read:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html>

In the volume (density-map) category, IMOD map:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#volume>

In the 3D object category, IMOD segmentation:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object>
... as further described here:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/imod.html>

(2) Chimera also has many options for map filtering and masking.  See the "volume guide"
<https://www.rbvi.ucsf.edu/chimera/data/tutorials/volumetour/volumetour.html>

...and specific documentation for many Volume-related tools (menu: Tools... Volume Data... Volume Viewer and others), commands "volume" "vop" and "mask" and others:
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#organization>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html>
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mask.html>

(3) You can hand-draw in Chimera by putting markers on slices with Volume Tracer and then combining the markers to make surfaces (also using that same tool). 
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/framevolpath.html> 
However, this is very labor-intensive and if you already have a surface created by some other means (e.g. reading in IMOD segmentation files) you can use that surface for masking instead of drawing it by hand.

(4) I don't understand the inverting problem so I couldn't say how to fix it, sorry.  If possible, please explain it more or give a specific example to help us better understand.

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


> On Dec 8, 2021, at 9:28 PM, 박시훈 via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear chimera-users community,
> I have questions about opening IMOD files in Chimera software.
> Can I open the IMOD  files (*.mod) in Chimera? Or, Can I make a hand-drawn mask file in Chimera? I could apply several filters and masks in my iso-surface map, however, I don't know how to apply these options in Chimera. Moreover,  the reconstructed tomograms were shown to the inverted iso-surface map unlike IMOD.. Can I re-invert the iso-surface map in Chimera?
> 
> Best regards
> Si Hoon Park
>