[chimerax-users] vop min/max threshold

[Elaine Meng]

Hi Kevin,
If you really want to set every value that is outside the 0.26-0.27 range to zero,  the command is:

vop threshold #2 min 0.26 set 0 max 0.27 setmax 0

The "set" keyword is for setting the new minimum, not the new maximum, as shown in the usage:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#threshold>

Also, be aware that your molmap map includes solvent, ligands, ions, etc.  If you don't want those, you'd need a narrower specification in the molmap command, e.g.

molmap #1 & protein 10

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Nov 9, 2021, at 4:31 PM, Stapleton kevin2017/4/3 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hello everyone! 
> 
> just trying to get my head around a small problem, but one my brain turns into spaghetti.   I am trying to save a density from molmap with a threshold range of given values.   
> 
> for example:
> 
> open 2gbp
> molmap #1 10
> 
> From the resulting density (now ID #2) I want to save the map at a very narrow threshold range.  for example the current range is 0.0-0.528.  But I would like to save the map with a "restricted" level of 0.26-0.27.  
> 
> I have been playing with the vop min/max threshold xxx set 0/1 commands but I keep getting turned around.  
> 
> here is what I did:
> 
> open 2gbp
> molmap #1 10  - produces a new map ID #2
> 
> vop threshold #2 minimum 0.26 set 0
> vop threshold #3 maximum 0.27 set 1
> 
> I used the set 0/1 because I want the range 0.26-0.27 to have the density values and anything outside of that to have zero.  Like a mask in relion.  But for my specific case relion_mask wont work as well. 
> 
> Somewhere I am turning the options around and it has my brain flattened.  Any help is appreciated. 
> 
> All the best and thanks for making my science life 1Million times easier with your wonderful program :-)
> 
> Kako
> 
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