[chimerax-users] Save a new map with trimmed zones (vop zone command)

[Elaine Meng]

Hi Steven,
You have to use the "newMap true" option with "volume zone" (aka "vop zone") for it to create a new map model, rather than just hiding the surface outside the zone.  It's explained here, or use command "help volume zone":
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#zone>

Then make sure you are actually saving the new map model, not the original one.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 24, 2021, at 11:04 AM, Steven Truong <sdt45 at cam.ac.uk> wrote:
> 
> Dear ChimeraX Admin.,
> Hello, I was hoping for some help on the save function for an electron-density map (.mrc file).  I have a density map (#0) that I trim using:
> 
> vop zone #0 nearAtoms #1 range 6
> 
> Essentially, I want to remove all the electron density that is not close to my structure (.pdb) #1.  Anything farther than 6 angstroms disappears, as expected.
> 
> However, when I proceed to do:
> 
> save newmap.mrc #0
> 
> I get the original map with the electron density I don’t want anymore.  It doesn’t seem like I can save the changes to the map, even though I see the changes in the interface.  It seems to want to save everything, ignoring the vop command.  Is there something else I’m missing here?
> Thank you for your help,
> Steven Truong
> Cambridge University
> sdt45 at cam.ac.uk