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

[박시훈]

Dear Elaine and Tom,
Thanks for your kind reply.
I am very happy to get good information, and I will try ChimeraX!

Best regards
Si Hoon Park


2021년 12월 10일 (금) 오후 3:12, Tom Goddard <goddard at sonic.net>님이 작성:

> 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.
>
>         Tom
>
>
> > 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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> >
>
>
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