[chimerax-users] volume onesmask usage question

[Alexis Rohou]

Hi Tom,

Excellent! Turning maps into masks is a pretty common task and I think this
will be my new favorite way to do it.

Thanks a lot!

Cheers,
Alexis

On Wed, Dec 11, 2019 at 2:48 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Alexis,
>
>   I added an onGrid option to the volume onesmask command.  So you can
> create a mask from the volume #1 surface on the grid of volume #1 using
>
> volume onesmask #1 ongrid #1
>
> This will be in tonight's ChimeraX builds.
>
> Tom
>
>
> On Dec 11, 2019, at 10:20 AM, Alexis Rohou <a.rohou at gmail.com> wrote:
>
> 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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