[chimerax-users] volume onesmask usage question

[Alexis Rohou]

Thanks Elaine,

Thanks for the clarification - I figured I wasn't reading things carefully
enough.

I worked with "volume mask" followed by "volume threshold" exactly as you
suggest, and it worked fine.

The "volume onesmask" as it is now stands out from most other volume
operations in that it creates an entirely new grid and doesn't even let us
stay on the same grid as the input. This makes it not-very-useful for my
regular work, but I'm sure there was a good reason initially.

Just saw Tom's email re. surface v volume distinction. Makes sense of
course, though I do think harmonizing the options across volume operations
would be nice if easily achievable.

Cheers,
Alexis

On Wed, Dec 11, 2019 at 10:15 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
>
>
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