[Chimera-users] Questions about IMOD files in Chimera software.
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:
> In the volume (density-map) category, IMOD map:
> In the 3D object category, IMOD segmentation:
> ... as further described here:
> (2) Chimera also has many options for map filtering and masking. See the "volume guide"
> ...and specific documentation for many Volume-related tools (menu: Tools... Volume Data... Volume Viewer and others), commands "volume" "vop" and "mask" and others:
> (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).
> 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 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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