[Chimera-users] Question about equivalent command in Chimera

[Thu Nguyen]

Thank you very much. My initial goal actually is to use ChimeraX commands.
I was writing a python script that utilizes ChimeraX commands to chop
individual chains from emdb map and its corresponding pdb structures.
However, I've just noticed that ChimeraX modules can only be used within
the ChimeraX application, I cannot use those commands in my python script
and run it like a regular python code. So I decided to stay with Chimera.
If there is a way to do it in ChimeraX, please let me know.
Thank you so much.

Best,
Thu

On Thu, Jul 28, 2022 at 3:31 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> For the other steps, you could use "open" to open the data, and "volume"
> command "save":
>
> open emdbID:12554
> open 7ns0
> vop cover #0 atomBox #1:.A1 pad 1.0
> volume #2 save ~/Desktop/12554_A1.mrc
>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/open.html#fetch>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>
> <
> https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output
> >
>
> Is there a specific reason you want to use Chimera instead of ChimeraX?
> I'm just curious -- if it's because of some Chimera feature, maybe I can
> suggest how to do it in ChimeraX.
>
> Elaine
>
> > On Jul 28, 2022, at 12:20 PM, Elaine Meng via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >
> > Hi Thu,
> > Chimera "vop cover"  is basically the same as ChimeraX "volume cover":
> >
> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#cover>
> >
> > However, ChimeraX is the newer program, faster on big data, with fancier
> display options (among many other advantages), so we generally recommend it
> over Chimera when both have the feature(s) you need.
> >
> > <https://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html>
> >
> > I hope this helps,
> > Elaine
> > -----
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >> On Jul 28, 2022, at 11:47 AM, Thu Nguyen via Chimera-users <
> chimera-users at cgl.ucsf.edu> wrote:
> >>
> >> Good afternoon,
> >> I want to ask if we have any command in Chimera that is similar to the
> command "volume cover" in ChimaraX. My goal is to create a map and pdb file
> of individual chains from the whole structure. For example:
> >>> open 12554 from emdb
> >>> open 7ns0
> >>> volume cover #1 atomBox #2/A1 pad 1.0
> >>> save 12554_A1.mrc models #3
> >> Could you tell me how I can do this using Chimera commands?
> >> Thank you very much.
> >> Best regards,
> >> Thu
>
>
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