[chimerax-users] volume onesmask usage question

[Alexis Rohou]

Hi Tom,

Old thread, but I was playing with volume onesmask #n onGrid #m today, and
it was not giving an output of the same dimensions as volume #m. Easy
enough to then do a volume resample onGrid, but this was not the behavior I
expected.

This was with 0.92 (2020-02-20, the palindrome version!) so not the latest,
but I wonder whether you can reproduce this and confirm whether that's
expected behavior.

Cheers,
Alexis

On Wed, Dec 11, 2019 at 4:22 PM Alexis Rohou <a.rohou at gmail.com> wrote:

> 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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