[Chimera-users] Question about equivalent command in Chimera

[Elaine Meng]

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