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

Tom Goddard goddard at sonic.net
Thu Dec 9 22:12:31 PST 2021

I suggest you use ChimeraX.  We have not developed Chimera for a long time and ChimeraX does all this map stuff and we are more likely to answer questions about ChimeraX.


> On Dec 9, 2021, at 10:55 AM, Elaine Meng via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 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
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