[chimerax-users] volume onesmask usage question

[Elaine Meng]

Hi Alexis,
The “remaining options” referred to those which are shown in the usage line for “volume onesmask” but not explained directly in that section:

• volume onesmask  surface-spec  [ border  B ] [ spacing  S | Sx,Sy,Sz ] [ pad  distance ] [ extend  N ] [ slab  width | d1,d2 ] [ invertMask  true | false ] [ axis  vector-spec ] [ sandwich  true | false ] [ fillOverlap  true | false ] [ modelId  M ]

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#onesmask>

Options not shown in that usage line are not available, at least as far as I knew when I wrote the documentation.  You can always check with the “usage” command, e.g. “usage volume onesmask”  will show all of its current options in the Log.

The differences are that mask has a fullmap option whereas onesmask has border and spacing options. I don’t know the rationale for the differences, sorry.  I imagine you might be able to get the result you wanted with a combination of operations, maybe using “volume mask” first and then “volume threshold” to reset all nonzero values to 1, but I don’t know how well that would work, and it seems unnecessarily indirect.  If I think of anything better, will let you know.  
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 11, 2019, at 9:58 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
> 
> Hi there,
> 
> I was trying to use "volume onesmask" to go quickly from a dusted surface of a low-pass-filtered volume to a mask volume with the same dimensions, spacing, etc. as the input map. 
> 
> I thought "fullmap" might be a way to achieve this (the doc says "The remaining options are the same as described for volume mask"), but I don't think that option actually works with "volume onesmask":
> 
> volume onesmask #3 fullmap true
> Expected a keyword
> 
> Is there a "onesmask"-like operation or set of options that creates an output volume that's on the same grid as the input volume?
> 
> Thanks,
> Alexis