[Chimera-users] Question about equivalent command in Chimera

[Tom Goddard]

Hi Thu,

  ChimeraX and Chimera both include Python in the application.  You can open a Python file in either program and it will be run.  You can also use a Python shell in either program, in ChimeraX the shell is shown by menu Tools / General / Shell, and in Chimera it is shown with menu Tools / General Controls / IDLE.  Neither program is setup to be used as a Python module in your own Python.  We plan to make such a module available through Conda or PyPi for ChimeraX in the next year.  There is a project called pychimera that tries to do this with Chimera, I have not used it,

	https://github.com/insilichem/pychimera

You can run Python code without the Chimera or ChimeraX gui from the command line, for example,

	chimerax --nogui myscript.py

We encourage you to use ChimeraX instead of Chimera because we have not developed Chimera for about 6 years and eventually Chimera will not work on new operating systems and your code will not longer work.  ChimeraX is also more capable than Chimera in many ways.

  Tom


> On Jul 28, 2022, at 12:49 PM, Thu Nguyen via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> 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 <mailto: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/open.html#fetch>>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>>
> <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#output <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 <mailto: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://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vop.html#cover>>
> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.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 <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 <mailto: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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