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

Tom Goddard goddard at sonic.net
Thu Dec 9 22:10:30 PST 2021

Hi Si Hoon Park,

It is common that tomograms have low values for high sample density and high values for low density.  The convention is that the values correspond to how much of the electron beam passes through the sample, so low density passes most of the beam gives high signal values.

When showing iso-surfaces of such an inverted map Chimera and ChimeraX draw surfaces at the box boundaries where the high values are next to the boundary because it is designed to show surfaces enclosing the high values.  You can turn those surfaces at the box boundaries off with command

	volume #1 capFaces false

as described in the docs

	https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#capfaces <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/volume.html#capfaces>

or you can make a new map with inverted values by multiplying by -1 with

	vop scale #1 factor -1

If your map is unsigned you might also need to specify a signed value type since this produces negative values

	vop scale #1 factor -1 valuetype float32

documented here




> 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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